From 824a73a5ed3054d3b4dc56096175d73b9f62abf0 Mon Sep 17 00:00:00 2001
From: PauAndrio <andriopau@gmail.com>
Date: Wed, 29 May 2024 13:17:27 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bioexcel?=
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-fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.editconf Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/editconf.gro to /tmp/biobb/unitests_107/editconf/290817ae-46f1-42ad-8c74-3a5592ee56e6\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Distance of the box to molecule:   1.00\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Centering molecule in the box.\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Box type: cubic\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright editconf -f /tmp/biobb/unitests_107/editconf/290817ae-46f1-42ad-8c74-3a5592ee56e6/editconf.gro -o /tmp/biobb/unitests_107/editconf/290817ae-46f1-42ad-8c74-3a5592ee56e6/output_gro.gro -bt cubic -d 1.0 -c\n\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:cmd_wrapper.py:52 Note that major changes are planned in future for editconf, to improve usability and utility.\nRead 1196 atoms\nVolume: 729.19 nm^3, corresponds to roughly 328100 electrons\nNo velocities found\n    system size :  5.722  6.526  3.712 (nm)\n    diameter    :  7.001               (nm)\n    center      :  4.500  4.501  4.501 (nm)\n    box vectors :  9.001  9.001  9.001 (nm)\n    box angles  :  90.00  90.00  90.00 (degrees)\n    box volume  : 729.19               (nm^3)\n    shift       :  0.000 -0.000 -0.000 (nm)\nnew center      :  4.500  4.500  4.500 (nm)\nnew box vectors :  9.001  9.001  9.001 (nm)\nnew box angles  :  90.00  90.00  90.00 (degrees)\nnew box volume  : 729.19               (nm^3)\n\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx editconf, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/editconf\nCommand line:\n  gmx -nobackup -nocopyright editconf -f /tmp/biobb/unitests_107/editconf/290817ae-46f1-42ad-8c74-3a5592ee56e6/editconf.gro -o /tmp/biobb/unitests_107/editconf/290817ae-46f1-42ad-8c74-3a5592ee56e6/output_gro.gro -bt cubic -d 1.0 -c\n\n\nGROMACS reminds you: &amp;quot;Gabba Gabba Hey!&amp;quot; (The Ramones)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_genion.py::TestGenion::test_genion&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_genion.py::TestGenion::test_genion&#34;, &#34;duration&#34;: &#34;202 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_genion.py::TestGenion::test_genion&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;202 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/genion/output_gro.gro\nChecking if empty file: /tmp/biobb/unitests_107/genion/output_top_zip.zip\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_107/genion/output_gro.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_genion.gro\n     SIZE_A: 3222684 bytes\n     SIZE_B: 3222684 bytes\n     TOLERANCE: 1.0%, Low: 3190457.16 bytes, High: 3254910.84 bytes\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_107/genion/output_top_zip.zip\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_genion.zip\n     SIZE_A: 375866 bytes\n     SIZE_B: 375866 bytes\n     TOLERANCE: 1.0%, Low: 372107.34 bytes, High: 379624.66 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     adcbb71e-1ffa-41cd-80f0-2319dd0779cb/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     adcbb71e-1ffa-41cd-80f0-2319dd0779cb/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     adcbb71e-1ffa-41cd-80f0-2319dd0779cb/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genion\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.genion Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genion.tpr to /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/genion/6e35878a-0789-40b3-822e-1c84dae606c7.stdin to /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genion.zip\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:174 [&amp;#x27;95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step8_gio_gio.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genion.zip\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:256 95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step4_p2g_p2g.itp\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:256 95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step8_gio_gio.top\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 To reach up 0.05 mol/litre concentration\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright genion -s /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055/genion.tpr -o /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055/output_gro.gro -p 95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step8_gio_gio.top -conc 0.05 -seed 1993 &amp;lt; /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055/6e35878a-0789-40b3-822e-1c84dae606c7.stdin\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:cmd_wrapper.py:52 Will try to add 22 NA ions and 22 CL ions.\nSelect a continuous group of solvent molecules\nSelected 13: &amp;#x27;SOL&amp;#x27;\n\nProcessing topology\nReplacing 44 solute molecules in topology file (95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step8_gio_gio.top)  by 22 NA and 22 CL ions.\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx genion, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genion\nCommand line:\n  gmx -nobackup -nocopyright genion -s /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055/genion.tpr -o /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055/output_gro.gro -p 95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step8_gio_gio.top -conc 0.05 -seed 1993\n\nReading file /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055/genion.tpr, VERSION 5.1.2 (single precision)\nReading file /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055/genion.tpr, VERSION 5.1.2 (single precision)\nGroup     0 (         System) has 71702 elements\nGroup     1 (        Protein) has  1196 elements\nGroup     2 (      Protein-H) has   618 elements\nGroup     3 (        C-alpha) has    79 elements\nGroup     4 (       Backbone) has   237 elements\nGroup     5 (      MainChain) has   317 elements\nGroup     6 (   MainChain+Cb) has   393 elements\nGroup     7 (    MainChain+H) has   396 elements\nGroup     8 (      SideChain) has   800 elements\nGroup     9 (    SideChain-H) has   301 elements\nGroup    10 (    Prot-Masses) has  1196 elements\nGroup    11 (    non-Protein) has 70506 elements\nGroup    12 (          Water) has 70506 elements\nGroup    13 (            SOL) has 70506 elements\nGroup    14 (      non-Water) has  1196 elements\nSelect a group: Number of (3-atomic) solvent molecules: 23502\nUsing random seed 1993.\nReplacing solvent molecule 8233 (atom 25895) with NA\nReplacing solvent molecule 1966 (atom 7094) with NA\nReplacing solvent molecule 5861 (atom 18779) with NA\nReplacing solvent molecule 3984 (atom 13148) with NA\nReplacing solvent molecule 17732 (atom 54392) with NA\nReplacing solvent molecule 12114 (atom 37538) with NA\nReplacing solvent molecule 19279 (atom 59033) with NA\nReplacing solvent molecule 13218 (atom 40850) with NA\nReplacing solvent molecule 15841 (atom 48719) with NA\nReplacing solvent molecule 7583 (atom 23945) with NA\nReplacing solvent molecule 13527 (atom 41777) with NA\nReplacing solvent molecule 16709 (atom 51323) with NA\nReplacing solvent molecule 1660 (atom 6176) with NA\nReplacing solvent molecule 14850 (atom 45746) with NA\nReplacing solvent molecule 5431 (atom 17489) with NA\nReplacing solvent molecule 20277 (atom 62027) with NA\nReplacing solvent molecule 9374 (atom 29318) with NA\nReplacing solvent molecule 4205 (atom 13811) with NA\nReplacing solvent molecule 15329 (atom 47183) with NA\nReplacing solvent molecule 208 (atom 1820) with NA\nReplacing solvent molecule 4341 (atom 14219) with NA\nReplacing solvent molecule 14344 (atom 44228) with NA\nReplacing solvent molecule 12731 (atom 39389) with CL\nReplacing solvent molecule 2246 (atom 7934) with CL\nReplacing solvent molecule 10972 (atom 34112) with CL\nReplacing solvent molecule 1350 (atom 5246) with CL\nReplacing solvent molecule 11157 (atom 34667) with CL\nReplacing solvent molecule 15670 (atom 48206) with CL\nReplacing solvent molecule 7900 (atom 24896) with CL\nReplacing solvent molecule 12147 (atom 37637) with CL\nReplacing solvent molecule 3049 (atom 10343) with CL\nReplacing solvent molecule 15083 (atom 46445) with CL\nReplacing solvent molecule 16474 (atom 50618) with CL\nReplacing solvent molecule 21986 (atom 67154) with CL\nReplacing solvent molecule 12088 (atom 37460) with CL\nReplacing solvent molecule 5004 (atom 16208) with CL\nReplacing solvent molecule 14621 (atom 45059) with CL\nReplacing solvent molecule 8784 (atom 27548) with CL\nReplacing solvent molecule 20066 (atom 61394) with CL\nReplacing solvent molecule 13479 (atom 41633) with CL\nReplacing solvent molecule 22247 (atom 67937) with CL\nReplacing solvent molecule 11017 (atom 34247) with CL\nReplacing solvent molecule 14301 (atom 44099) with CL\nReplacing solvent molecule 6548 (atom 20840) with CL\n\n\nGROMACS reminds you: &amp;quot;Gabba Gabba Hey!&amp;quot; (The Ramones)\n\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_107/genion/686643bb-31d1-4374-9590-568cf3f4b055/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:203 Ignored file 95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/amber99sb-ildn.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:203 Ignored file 95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/amber99sb-ildn.ff/spce.itp\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:203 Ignored file 95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/amber99sb-ildn.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:149 [&amp;#x27;95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step8_gio_gio.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:150 to: /tmp/biobb/unitests_107/genion/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Removed: [&amp;#x27;95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;95176f1c-cbd0-4d52-96d9-68b50f4d7ca5/A.Lys58Glu_step8_gio_gio.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr&#34;, &#34;duration&#34;: &#34;566 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;566 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/genrestr/output_itp.itp\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_107/genrestr/output_itp.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_genrestr.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     c8d50fbc-290b-4794-ab27-45492355c3be/log.out:cmd_wrapper.py:33 gmx  -nobackup -nocopyright -version\n\nINFO     c8d50fbc-290b-4794-ab27-45492355c3be/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     c8d50fbc-290b-4794-ab27-45492355c3be/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genrestr\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.genrestr Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genrestr.gro to /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genrestr.ndx to /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/genrestr/7b978307-3732-400b-9523-fdefe5b05984.stdin to /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:cmd_wrapper.py:33 gmx  -nobackup -nocopyright genrestr -f /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f/genrestr.gro -o /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f/output_itp.itp -fc 500 500 500 -n /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f/genrestr.ndx &amp;lt; /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f/7b978307-3732-400b-9523-fdefe5b05984.stdin\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:cmd_wrapper.py:52 Select group to position restrain\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx genrestr, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genrestr\nCommand line:\n  gmx -nobackup -nocopyright genrestr -f /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f/genrestr.gro -o /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f/output_itp.itp -fc 500 500 500 -n /tmp/biobb/unitests_107/genrestr/fd5c22fd-2d01-41b7-80cd-200d2893f12f/genrestr.ndx\n\n\nReading structure file\nGroup     0 (         System) has 31633 elements\nGroup     1 (        Protein) has 31633 elements\nGroup     2 (      Protein-H) has 15652 elements\nGroup     3 (        C-alpha) has  2068 elements\nGroup     4 (       Backbone) has  6204 elements\nGroup     5 (      MainChain) has  8276 elements\nGroup     6 (   MainChain+Cb) has 10164 elements\nGroup     7 (    MainChain+H) has 10248 elements\nGroup     8 (      SideChain) has 21385 elements\nGroup     9 (    SideChain-H) has  7376 elements\nGroup    10 (    chA_&amp;amp;_r_513) has    20 elements\nGroup    11 (    chB_&amp;amp;_r_513) has    20 elements\nSelect a group: \nGROMACS reminds you: &amp;quot;Gabba Gabba Hey!&amp;quot; (The Ramones)\n\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr_noNDX&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr_noNDX&#34;, &#34;duration&#34;: &#34;931 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr_noNDX&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;931 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/genrestr/output_itp.itp\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_107/genrestr/output_itp.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_genrestr_noNDX.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     6443547a-ce15-44b7-b9c8-69504f83bc6f/log.out:cmd_wrapper.py:33 gmx  -nobackup -nocopyright -version\n\nINFO     6443547a-ce15-44b7-b9c8-69504f83bc6f/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     6443547a-ce15-44b7-b9c8-69504f83bc6f/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genrestr\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:file_utils.py:391 Executing biobb_gromacs.gromacs.genrestr Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genrestr.gro to /tmp/biobb/unitests_107/genrestr/18a29b36-68d6-458e-8616-858399d39840\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/genrestr/3b3702d0-582e-4948-b20e-afb0fedb1219.stdin to /tmp/biobb/unitests_107/genrestr/18a29b36-68d6-458e-8616-858399d39840\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:cmd_wrapper.py:33 gmx  -nobackup -nocopyright genrestr -f /tmp/biobb/unitests_107/genrestr/18a29b36-68d6-458e-8616-858399d39840/genrestr.gro -o /tmp/biobb/unitests_107/genrestr/18a29b36-68d6-458e-8616-858399d39840/output_itp.itp -fc 500 500 500 &amp;lt; /tmp/biobb/unitests_107/genrestr/18a29b36-68d6-458e-8616-858399d39840/3b3702d0-582e-4948-b20e-afb0fedb1219.stdin\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:cmd_wrapper.py:52 Select group to position restrain\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.err:cmd_wrapper.py:60                :-) GROMACS - gmx genrestr, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genrestr\nCommand line:\n  gmx -nobackup -nocopyright genrestr -f /tmp/biobb/unitests_107/genrestr/18a29b36-68d6-458e-8616-858399d39840/genrestr.gro -o /tmp/biobb/unitests_107/genrestr/18a29b36-68d6-458e-8616-858399d39840/output_itp.itp -fc 500 500 500\n\n\nReading structure file\nGroup     0 (         System) has 71690 elements\nGroup     1 (        Protein) has  1196 elements\nGroup     2 (      Protein-H) has   618 elements\nGroup     3 (        C-alpha) has    79 elements\nGroup     4 (       Backbone) has   237 elements\nGroup     5 (      MainChain) has   317 elements\nGroup     6 (   MainChain+Cb) has   393 elements\nGroup     7 (    MainChain+H) has   396 elements\nGroup     8 (      SideChain) has   800 elements\nGroup     9 (    SideChain-H) has   301 elements\nGroup    10 (    Prot-Masses) has  1196 elements\nGroup    11 (    non-Protein) has 70494 elements\nGroup    12 (          Water) has 70488 elements\nGroup    13 (            SOL) has 70488 elements\nGroup    14 (      non-Water) has  1202 elements\nGroup    15 (            Ion) has     6 elements\nGroup    16 (             NA) has     6 elements\nGroup    17 ( Water_and_ions) has 70494 elements\nSelect a group: \nGROMACS reminds you: &amp;quot;I&amp;#x27;m a Jerk&amp;quot; (F. Black)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py::TestGmxselect::test_select&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py::TestGmxselect::test_select&#34;, &#34;duration&#34;: &#34;240 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py::TestGmxselect::test_select&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;240 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/gmxselect/output_ndx.ndx\nComparing: \n        File_A: /tmp/biobb/unitests_107/gmxselect/output_ndx.ndx\n        File_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_select.ndx\n        File_A hash: b&amp;#x27;^v&amp;gt;\\xac\\x07\\xf2\\tpB+\\xc57\\xf9X\\xc8\\xd3\\xb6\\xaf\\xfb{\\x18@\\xe7\\x8e\\xaeF\\x00b\\xea\\xc8\\x19$&amp;#x27;\n        File_B hash: b&amp;#x27;^v&amp;gt;\\xac\\x07\\xf2\\tpB+\\xc57\\xf9X\\xc8\\xd3\\xb6\\xaf\\xfb{\\x18@\\xe7\\x8e\\xaeF\\x00b\\xea\\xc8\\x19$&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     d7b08b27-1974-4e6e-8243-0d15532c0c1c/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     d7b08b27-1974-4e6e-8243-0d15532c0c1c/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     d7b08b27-1974-4e6e-8243-0d15532c0c1c/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/gmxselect\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.gmxselect Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/make_ndx.tpr to /tmp/biobb/unitests_107/gmxselect/c6d26a9b-710b-403b-ab86-0d80c86d44c9\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright select -s /tmp/biobb/unitests_107/gmxselect/c6d26a9b-710b-403b-ab86-0d80c86d44c9/make_ndx.tpr -on /tmp/biobb/unitests_107/gmxselect/c6d26a9b-710b-403b-ab86-0d80c86d44c9/output_ndx.ndx -select &amp;#x27;&amp;quot;Mynewgroup&amp;quot; group &amp;quot;Protein-H&amp;quot; and not same residue as within 0.4 of resname ARG&amp;#x27;\n\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx select, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/gmxselect\nCommand line:\n  gmx -nobackup -nocopyright select -s /tmp/biobb/unitests_107/gmxselect/c6d26a9b-710b-403b-ab86-0d80c86d44c9/make_ndx.tpr -on /tmp/biobb/unitests_107/gmxselect/c6d26a9b-710b-403b-ab86-0d80c86d44c9/output_ndx.ndx -select &amp;#x27;&amp;quot;Mynewgroup&amp;quot; group &amp;quot;Protein-H&amp;quot; and not same residue as within 0.4 of resname ARG&amp;#x27;\n\nReading file /tmp/biobb/unitests_107/gmxselect/c6d26a9b-710b-403b-ab86-0d80c86d44c9/make_ndx.tpr, VERSION 5.1.2 (single precision)\nReading file /tmp/biobb/unitests_107/gmxselect/c6d26a9b-710b-403b-ab86-0d80c86d44c9/make_ndx.tpr, VERSION 5.1.2 (single precision)\nAnalyzed topology coordinates\n\nGROMACS reminds you: &amp;quot;In the Meantime, Take Care of Yourself aaand Eachother&amp;quot; (J. Springer)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_grompp.py::TestGrompp::test_grompp&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_grompp.py::TestGrompp::test_grompp&#34;, &#34;duration&#34;: &#34;498 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_grompp.py::TestGrompp::test_grompp&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;498 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/grompp/output_tpr.tpr\nComparing GROMACS files:\nFILE_A: /tmp/biobb/unitests_107/grompp/output_tpr.tpr\nFILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr\n\ncmd_wrapper commnand print: gmx check -s1 /tmp/biobb/unitests_107/grompp/output_tpr.tpr -s2 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr &amp;gt; check_result.out\nExit, code 0\nResult file: /tmp/biobb/unitests_107/grompp/check_result.out\n\n------------------------------ Captured log call -------------------------------\nINFO     0b901cc9-cc5d-493e-9d49-6dd6ace27d4f/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     0b901cc9-cc5d-493e-9d49-6dd6ace27d4f/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     0b901cc9-cc5d-493e-9d49-6dd6ace27d4f/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.grompp Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.gro to /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.zip\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:174 [&amp;#x27;/tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/A.Lys58Glu_step6_sol_sol.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.zip\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:256 /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/A.Lys58Glu_step4_p2g_p2g.itp\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:256 /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/A.Lys58Glu_step6_sol_sol.top\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright grompp -f /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/grompp.mdp -c /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/grompp.gro -r /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/grompp.gro -p /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/A.Lys58Glu_step6_sol_sol.top -o /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/output_tpr.tpr -po mdout.mdp -maxwarn 1\n\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:cmd_wrapper.py:52 Generated 2145 of the 2145 non-bonded parameter combinations\n\nGenerated 2145 of the 2145 1-4 parameter combinations\n\nExcluding 3 bonded neighbours molecule type &amp;#x27;Protein_chain_A&amp;#x27;\n\nExcluding 2 bonded neighbours molecule type &amp;#x27;SOL&amp;#x27;\n\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\nJ. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof\nQuantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net\nCharge\nJ. Chem. Theory Comput. 10 (2014) pp. 381-393\n-------- -------- --- Thank You --- -------- --------\n\nAnalysing residue names:\nThere are:    79    Protein residues\nThere are: 23502      Water residues\nAnalysing Protein...\n\nThe largest distance between excluded atoms is 0.417 nm\nCalculating fourier grid dimensions for X Y Z\nUsing a fourier grid of 80x80x80, spacing 0.113 0.113 0.113\n\nEstimate for the relative computational load of the PME mesh part: 0.23\n\nThis run will generate roughly 5 Mb of data\n\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx grompp, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp\nCommand line:\n  gmx -nobackup -nocopyright grompp -f /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/grompp.mdp -c /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/grompp.gro -r /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/grompp.gro -p /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/A.Lys58Glu_step6_sol_sol.top -o /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/output_tpr.tpr -po mdout.mdp -maxwarn 1\n\nIgnoring obsolete mdp entry &amp;#x27;ns-type&amp;#x27;\nGenerating 1-4 interactions: fudge = 0.5\n\nNOTE 1 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  System has non-zero total charge: -6.000000\n  Total charge should normally be an integer. See\n  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n  for discussion on how close it should be to an integer.\n  \n\n\n\nWARNING 1 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  You are using Ewald electrostatics in a system with net charge. This can\n  lead to severe artifacts, such as ions moving into regions with low\n  dielectric, due to the uniform background charge. We suggest to\n  neutralize your system with counter ions, possibly in combination with a\n  physiological salt concentration.\n\n\nNOTE 2 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  The bond in molecule-type Protein_chain_A between atoms 10 OG and 11 HG\n  has an estimated oscillational period of 9.0e-03 ps, which is less than\n  10 times the time step of 1.0e-03 ps.\n  Maybe you forgot to change the constraints mdp option.\n\nNumber of degrees of freedom in T-Coupling group rest is 144597.00\n\nNOTE 3 [file /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/grompp.mdp]:\n  NVE simulation with an initial temperature of zero: will use a Verlet\n  buffer of 10%. Check your energy drift!\n\n\nNOTE 4 [file /tmp/biobb/unitests_107/grompp/c3a0b988-26ca-4c62-aec9-6b6fd0d37002/grompp.mdp]:\n  Removing center of mass motion in the presence of position restraints\n  might cause artifacts. When you are using position restraints to\n  equilibrate a macro-molecule, the artifacts are usually negligible.\n\n\nThere were 4 notes\n\nThere was 1 warning\n\nGROMACS reminds you: &amp;quot;In the Meantime, Take Care of Yourself aaand Eachother&amp;quot; (J. Springer)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py::TestGromppMdrun::test_grompp_mdrun&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py::TestGromppMdrun::test_grompp_mdrun&#34;, &#34;duration&#34;: &#34;00:01:09&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py::TestGromppMdrun::test_grompp_mdrun&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:09&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/grompp_mdrun/output_trr_path.trr\nComparing GROMACS files:\nFILE_A: /tmp/biobb/unitests_107/grompp_mdrun/output_trr_path.trr\nFILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_grompp_mdrun.trr\n\ncmd_wrapper commnand print: echo &amp;quot;Protein Protein&amp;quot; | gmx rms -s /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.gro -f /tmp/biobb/unitests_107/grompp_mdrun/output_trr_path.trr -f2 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_grompp_mdrun.trr -xvg none\nExit, code 0\nResult file: /tmp/biobb/unitests_107/grompp_mdrun/rmsd.xvg\nChecking if empty file: /tmp/biobb/unitests_107/grompp_mdrun/output_gro_path.gro\nChecking if empty file: /tmp/biobb/unitests_107/grompp_mdrun/output_edr_path.edr\nChecking if empty file: /tmp/biobb/unitests_107/grompp_mdrun/output_log_path.log\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log.out:file_utils.py:391 Calling Grompp class\nINFO     b11532fd-979f-406d-a03f-0120ce7b6100/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     b11532fd-979f-406d-a03f-0120ce7b6100/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     b11532fd-979f-406d-a03f-0120ce7b6100/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp_mdrun\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:391 Executing biobb_gromacs.gromacs.grompp Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.gro to /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.zip\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:174 [&amp;#x27;/tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/A.Lys58Glu_step6_sol_sol.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.zip\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:256 /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/A.Lys58Glu_step4_p2g_p2g.itp\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:256 /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/A.Lys58Glu_step6_sol_sol.top\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright grompp -f /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/grompp.mdp -c /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/grompp.gro -r /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/grompp.gro -p /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/A.Lys58Glu_step6_sol_sol.top -o /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/internal.tpr -po mdout.mdp -maxwarn 1\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:cmd_wrapper.py:52 Generated 2145 of the 2145 non-bonded parameter combinations\n\nGenerated 2145 of the 2145 1-4 parameter combinations\n\nExcluding 3 bonded neighbours molecule type &amp;#x27;Protein_chain_A&amp;#x27;\n\nturning H bonds into constraints...\n\nExcluding 2 bonded neighbours molecule type &amp;#x27;SOL&amp;#x27;\n\nturning H bonds into constraints...\n\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\nJ. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof\nQuantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net\nCharge\nJ. Chem. Theory Comput. 10 (2014) pp. 381-393\n-------- -------- --- Thank You --- -------- --------\n\nAnalysing residue names:\nThere are:    79    Protein residues\nThere are: 23502      Water residues\nAnalysing Protein...\n\nThe largest distance between excluded atoms is 0.417 nm\n\nDetermining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n\nCalculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm\n\nSet rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm\n\nNote that mdrun will redetermine rlist based on the actual pair-list setup\nCalculating fourier grid dimensions for X Y Z\nUsing a fourier grid of 80x80x80, spacing 0.113 0.113 0.113\n\nEstimate for the relative computational load of the PME mesh part: 0.27\n\nThis run will generate roughly 11 Mb of data\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.err:cmd_wrapper.py:60                 :-) GROMACS - gmx grompp, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp_mdrun\nCommand line:\n  gmx -nobackup -nocopyright grompp -f /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/grompp.mdp -c /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/grompp.gro -r /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/grompp.gro -p /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/A.Lys58Glu_step6_sol_sol.top -o /tmp/biobb/unitests_107/grompp_mdrun/dc261d51-3da7-49dd-a6f2-c12366e4f94b/internal.tpr -po mdout.mdp -maxwarn 1\n\nIgnoring obsolete mdp entry &amp;#x27;ns-type&amp;#x27;\nGenerating 1-4 interactions: fudge = 0.5\n\nNOTE 1 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  System has non-zero total charge: -6.000000\n  Total charge should normally be an integer. See\n  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n  for discussion on how close it should be to an integer.\n  \n\n\n\nWARNING 1 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  You are using Ewald electrostatics in a system with net charge. This can\n  lead to severe artifacts, such as ions moving into regions with low\n  dielectric, due to the uniform background charge. We suggest to\n  neutralize your system with counter ions, possibly in combination with a\n  physiological salt concentration.\n\nNumber of degrees of freedom in T-Coupling group Protein is 3009.94\nNumber of degrees of freedom in T-Coupling group non-Protein is 141009.06\n\nThere was 1 note\n\nThere was 1 warning\n\nGROMACS reminds you: &amp;quot;In the Meantime, Take Care of Yourself aaand Eachother&amp;quot; (J. Springer)\n\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log.out:file_utils.py:391 Grompp return code: 0\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log.out:file_utils.py:391 Grompp return code is correct. Calling MDRun class\nINFO     f62adf1c-6395-49f9-a0ba-a4944d99de7f/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     f62adf1c-6395-49f9-a0ba-a4944d99de7f/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     f62adf1c-6395-49f9-a0ba-a4944d99de7f/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp_mdrun\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:file_utils.py:391 Executing biobb_gromacs.gromacs.mdrun Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:file_utils.py:391 Copy: e2feaba5-417d-4005-93b4-14d45e2910a1/internal.tpr to /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:file_utils.py:391 User added number of gmx threads: 0\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright mdrun -o /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/output_trr_path.trr -s /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/internal.tpr -c /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/output_gro_path.gro -e /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/output_edr_path.edr -g /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/output_log_path.log -nt 0\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.err:cmd_wrapper.py:60                 :-) GROMACS - gmx mdrun, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp_mdrun\nCommand line:\n  gmx -nobackup -nocopyright mdrun -o /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/output_trr_path.trr -s /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/internal.tpr -c /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/output_gro_path.gro -e /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/output_edr_path.edr -g /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/output_log_path.log -nt 0\n\nReading file /tmp/biobb/unitests_107/grompp_mdrun/d4821ebb-c7ea-44ea-9c60-0bf369a69cdd/internal.tpr, VERSION 2022.2-conda_forge (single precision)\nChanging nstlist from 10 to 100, rlist from 1 to 1\n\nUsing 1 MPI thread\nUsing 4 OpenMP threads \n\nstarting mdrun &amp;#x27;Protein in water&amp;#x27;\n5000 steps,      0.5 ps.\n\nWriting final coordinates.\n\n               Core t (s)   Wall t (s)        (%)\n       Time:      261.868       65.467      400.0\n                 (ns/day)    (hour/ns)\nPerformance:        0.660       36.363\n\nGROMACS reminds you: &amp;quot;When the universe has expanded, time will contract&amp;quot; (Franz Ferdinand)\n\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log.out:file_utils.py:391 MDRun return code: 0\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py::TestMakeNdx::test_make_ndx&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py::TestMakeNdx::test_make_ndx&#34;, &#34;duration&#34;: &#34;109 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py::TestMakeNdx::test_make_ndx&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;109 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/make_ndx/output_ndx.ndx\nComparing: \n        File_A: /tmp/biobb/unitests_107/make_ndx/output_ndx.ndx\n        File_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_make_ndx_protein_dna.ndx\n        File_A hash: b&amp;#x27;\\xd7i\\x10P\\xf5\\x975\\xfe&amp;lt;X\\xaaf\\x83H\\x14i\\x0f\\xd1=I\\xa3\\xb92?\\xaa\\xf7\\x10\\xf0U\\xdb\\x90\\xa9&amp;#x27;\n        File_B hash: b&amp;#x27;\\xd7i\\x10P\\xf5\\x975\\xfe&amp;lt;X\\xaaf\\x83H\\x14i\\x0f\\xd1=I\\xa3\\xb92?\\xaa\\xf7\\x10\\xf0U\\xdb\\x90\\xa9&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     530f062d-ee18-4bad-ac84-3d1a07395753/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     530f062d-ee18-4bad-ac84-3d1a07395753/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     530f062d-ee18-4bad-ac84-3d1a07395753/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/make_ndx\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.make_ndx Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/make_ndx_protein_dna.pdb to /tmp/biobb/unitests_107/make_ndx/40b2d37d-7186-412a-a942-7036d2adca30\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/make_ndx/18654a48-fff4-463c-98e6-7041494666ca.stdin to /tmp/biobb/unitests_107/make_ndx/40b2d37d-7186-412a-a942-7036d2adca30\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright make_ndx -f /tmp/biobb/unitests_107/make_ndx/40b2d37d-7186-412a-a942-7036d2adca30/make_ndx_protein_dna.pdb -o /tmp/biobb/unitests_107/make_ndx/40b2d37d-7186-412a-a942-7036d2adca30/output_ndx.ndx &amp;lt; /tmp/biobb/unitests_107/make_ndx/40b2d37d-7186-412a-a942-7036d2adca30/18654a48-fff4-463c-98e6-7041494666ca.stdin\n\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:cmd_wrapper.py:52 Going to read 0 old index file(s)\nAnalysing residue names:\nThere are:   292    Protein residues\nThere are:    46        DNA residues\nAnalysing Protein...\n\n  0 System              :  3063 atoms\n  1 Protein             :  2126 atoms\n  2 Protein-H           :  2126 atoms\n  3 C-alpha             :   292 atoms\n  4 Backbone            :   876 atoms\n  5 MainChain           :  1168 atoms\n  6 MainChain+Cb        :  1448 atoms\n  7 MainChain+H         :  1168 atoms\n  8 SideChain           :   958 atoms\n  9 SideChain-H         :   958 atoms\n 10 Prot-Masses         :  2126 atoms\n 11 non-Protein         :   937 atoms\n 12 DNA                 :   937 atoms\n\n nr : group      &amp;#x27;!&amp;#x27;: not  &amp;#x27;name&amp;#x27; nr name   &amp;#x27;splitch&amp;#x27; nr    Enter: list groups\n &amp;#x27;a&amp;#x27;: atom       &amp;#x27;&amp;amp;&amp;#x27;: and  &amp;#x27;del&amp;#x27; nr         &amp;#x27;splitres&amp;#x27; nr   &amp;#x27;l&amp;#x27;: list residues\n &amp;#x27;t&amp;#x27;: atom type  &amp;#x27;|&amp;#x27;: or   &amp;#x27;keep&amp;#x27; nr        &amp;#x27;splitat&amp;#x27; nr    &amp;#x27;h&amp;#x27;: help\n &amp;#x27;r&amp;#x27;: residue              &amp;#x27;res&amp;#x27; nr         &amp;#x27;chain&amp;#x27; char\n &amp;quot;name&amp;quot;: group             &amp;#x27;case&amp;#x27;: case sensitive           &amp;#x27;q&amp;#x27;: save and quit\n &amp;#x27;ri&amp;#x27;: residue index\n\n&amp;gt; \nFound 1808 atoms with name C*\n\n 13 C*                  :  1808 atoms\n\n&amp;gt; \nCopied index group 0 &amp;#x27;System&amp;#x27;\nCopied index group 13 &amp;#x27;C*&amp;#x27;\nComplemented group: 1255 atoms\nMerged two groups with AND: 3063 1255 -&amp;gt; 1255\n\n 14 System_&amp;amp;_!C*        :  1255 atoms\n\n&amp;gt; \n\n&amp;gt; \n\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx make_ndx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/make_ndx\nCommand line:\n  gmx -nobackup -nocopyright make_ndx -f /tmp/biobb/unitests_107/make_ndx/40b2d37d-7186-412a-a942-7036d2adca30/make_ndx_protein_dna.pdb -o /tmp/biobb/unitests_107/make_ndx/40b2d37d-7186-412a-a942-7036d2adca30/output_ndx.ndx\n\n\nReading structure file\n\nGROMACS reminds you: &amp;quot;What Kind Of Guru are You, Anyway ?&amp;quot; (F. Zappa)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py::TestMdrun::test_mdrun&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py::TestMdrun::test_mdrun&#34;, &#34;duration&#34;: &#34;00:01:50&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py::TestMdrun::test_mdrun&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:50&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/mdrun/output_trr_path.trr\nComparing GROMACS files:\nFILE_A: /tmp/biobb/unitests_107/mdrun/output_trr_path.trr\nFILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_mdrun.trr\n\ncmd_wrapper commnand print: echo &amp;quot;Protein Protein&amp;quot; | gmx rms -s /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/mdrun.tpr -f /tmp/biobb/unitests_107/mdrun/output_trr_path.trr -f2 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_mdrun.trr -xvg none\nExit, code 0\nResult file: /tmp/biobb/unitests_107/mdrun/rmsd.xvg\nChecking if empty file: /tmp/biobb/unitests_107/mdrun/output_gro_path.gro\nChecking if empty file: /tmp/biobb/unitests_107/mdrun/output_edr_path.edr\nChecking if empty file: /tmp/biobb/unitests_107/mdrun/output_log_path.log\n\n------------------------------ Captured log call -------------------------------\nINFO     793f14a3-a282-4ed1-b3b0-16c758e3db31/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     793f14a3-a282-4ed1-b3b0-16c758e3db31/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     793f14a3-a282-4ed1-b3b0-16c758e3db31/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/mdrun\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.mdrun Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/mdrun.tpr to /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:file_utils.py:391 User added number of gmx threads: 0\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright mdrun -o /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/output_trr_path.trr -s /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/mdrun.tpr -c /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/output_gro_path.gro -e /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/output_edr_path.edr -g /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/output_log_path.log -nt 0\n\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx mdrun, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/mdrun\nCommand line:\n  gmx -nobackup -nocopyright mdrun -o /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/output_trr_path.trr -s /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/mdrun.tpr -c /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/output_gro_path.gro -e /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/output_edr_path.edr -g /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/output_log_path.log -nt 0\n\nReading file /tmp/biobb/unitests_107/mdrun/a5ebab88-0c6e-49ec-83c9-67dc81bd83ab/mdrun.tpr, VERSION 2018.1 (single precision)\nNote: file tpx version 112, software tpx version 127\nChanging nstlist from 10 to 40, rlist from 1 to 1.096\n\nUsing 1 MPI thread\nUsing 4 OpenMP threads \n\nstarting mdrun &amp;#x27;Protein in water&amp;#x27;\n15000 steps,     30.0 ps.\n\nWriting final coordinates.\n\n               Core t (s)   Wall t (s)        (%)\n       Time:      430.587      107.647      400.0\n                 (ns/day)    (hour/ns)\nPerformance:       24.080        0.997\n\nGROMACS reminds you: &amp;quot;The Nobel Prize is fine, but the drugs I&amp;#x27;ve developed are rewards in themselves.&amp;quot; (Gertrude Elion)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py::TestPdb2gmx::test_pdb2gmx&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py::TestPdb2gmx::test_pdb2gmx&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py::TestPdb2gmx::test_pdb2gmx&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/pdb2gmx/output_top_zip.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_107/pdb2gmx/output_top_zip.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_pdb2gmx.zip\nComparing TOP/ITP:\n     FILE_A: 1fdfdfcf-6fce-4e84-bdf0-79219a527c85/pdb2gmx_p2g.top\n     FILE_B: de02356a-82be-473e-a2bf-5a3dd917eb3f/pdb2gmx_p2g.top\nComparing TOP/ITP:\n     FILE_A: 1fdfdfcf-6fce-4e84-bdf0-79219a527c85/pdb2gmx_posre.itp\n     FILE_B: de02356a-82be-473e-a2bf-5a3dd917eb3f/pdb2gmx_posre.itp\nChecking if empty file: /tmp/biobb/unitests_107/pdb2gmx/output_gro.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_107/pdb2gmx/output_gro.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_pdb2gmx.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     54664cbd-a35d-4395-906d-3d2615ae97a8/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     54664cbd-a35d-4395-906d-3d2615ae97a8/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     54664cbd-a35d-4395-906d-3d2615ae97a8/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/pdb2gmx\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.pdb2gmx Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/egfr.pdb to /tmp/biobb/unitests_107/pdb2gmx/22eeaa5c-8a04-41a7-a5fd-d456d9ce52af\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/pdb2gmx/8ed8ec8e-b809-44ad-9f3c-2499e5a801e0.stdin to /tmp/biobb/unitests_107/pdb2gmx/22eeaa5c-8a04-41a7-a5fd-d456d9ce52af\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright pdb2gmx -f /tmp/biobb/unitests_107/pdb2gmx/22eeaa5c-8a04-41a7-a5fd-d456d9ce52af/egfr.pdb -o /tmp/biobb/unitests_107/pdb2gmx/22eeaa5c-8a04-41a7-a5fd-d456d9ce52af/output_gro.gro -p pdb2gmx_p2g.top -water spce -ff amber99sb-ildn -i pdb2gmx_posre.itp -his &amp;lt; /tmp/biobb/unitests_107/pdb2gmx/22eeaa5c-8a04-41a7-a5fd-d456d9ce52af/8ed8ec8e-b809-44ad-9f3c-2499e5a801e0.stdin\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:cmd_wrapper.py:52 Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff\n\ngoing to rename amber99sb-ildn.ff/aminoacids.r2b\n\ngoing to rename amber99sb-ildn.ff/dna.r2b\n\ngoing to rename amber99sb-ildn.ff/rna.r2b\nReading /tmp/biobb/unitests_107/pdb2gmx/22eeaa5c-8a04-41a7-a5fd-d456d9ce52af/egfr.pdb...\nRead &amp;#x27;Protein in water&amp;#x27;, 4698 atoms\n\nAnalyzing pdb file\nSplitting chemical chains based on TER records or chain id changing.\n\nThere are 1 chains and 0 blocks of water and 291 residues with 4698 atoms\n\n  chain  #res #atoms\n\n  1 &amp;#x27; &amp;#x27;   291   4698  \n\nAll occupancies are one\n\nReading residue database... (Amber99sb-ildn)\n\nProcessing chain 1 (4698 atoms, 291 residues)\nWhich HISTIDINE type do you want for residue 80\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 112\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 142\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 157\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 177\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 195\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 200\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:\nIdentified residue ALA694 as a starting terminus.\n\nIdentified residue ASP984 as a ending terminus.\n\nChecking for duplicate atoms....\n\nGenerating any missing hydrogen atoms and/or adding termini.\n\nNow there are 291 residues with 4698 atoms\n\nMaking bonds...\n\nNumber of bonds was 4750, now 4749\n\nGenerating angles, dihedrals and pairs...\n\nMaking cmap torsions...\n\nThere are 13015 dihedrals,  885 impropers, 8643 angles\n          12439 pairs,     4749 bonds and     0 virtual sites\n\nTotal mass 33034.844 a.m.u.\n\nTotal charge 1.000 e\n\nWriting topology\n\nWriting coordinate file...\n\n\t\t--------- PLEASE NOTE ------------\n\nYou have successfully generated a topology from: /tmp/biobb/unitests_107/pdb2gmx/22eeaa5c-8a04-41a7-a5fd-d456d9ce52af/egfr.pdb.\n\nThe Amber99sb-ildn force field and the spce water model are used.\n\n\t\t--------- ETON ESAELP ------------\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx pdb2gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/pdb2gmx\nCommand line:\n  gmx -nobackup -nocopyright pdb2gmx -f /tmp/biobb/unitests_107/pdb2gmx/22eeaa5c-8a04-41a7-a5fd-d456d9ce52af/egfr.pdb -o /tmp/biobb/unitests_107/pdb2gmx/22eeaa5c-8a04-41a7-a5fd-d456d9ce52af/output_gro.gro -p pdb2gmx_p2g.top -water spce -ff amber99sb-ildn -i pdb2gmx_posre.itp -his\n\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/dna.r2b\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/rna.r2b\nAll occupancies are one\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/dna.rtp\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/rna.rtp\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/dna.hdb\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/rna.hdb\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb\n8 out of 8 lines of specbond.dat converted successfully\nSpecial Atom Distance matrix:\n                  MET695  MET766 HISD773  CYS775  CYS781  MET793  CYS797\n                    SD23  SD1165 NE21261  SG1289  SG1388  SD1581  SG1636\n  MET766  SD1165   2.050\n HISD773 NE21261   2.326   1.712\n  CYS775  SG1289   2.164   0.449   1.373\n  CYS781  SG1388   2.773   1.629   3.094   1.807\n  MET793  SD1581   2.494   0.945   1.126   0.509   2.146\n  CYS797  SG1636   3.260   1.426   1.690   1.216   2.628   0.992\n HISD805 NE21778   4.161   2.554   2.115   2.186   3.416   1.721   1.389\n  CYS818  SG1989   3.418   2.358   1.312   2.084   3.856   1.769   1.505\n  MET825  SD2094   2.430   1.467   1.209   1.395   3.095   1.413   1.411\n HISE835 NE22276   2.416   1.048   1.540   1.110   2.637   1.276   1.201\n HISE850 NE22524   2.350   1.478   0.515   1.070   2.695   0.750   1.522\n HISD870 NE22846   3.369   2.871   3.404   3.131   4.127   3.395   3.126\n  MET881  SD3017   3.150   2.072   2.344   2.185   3.555   2.299   1.872\n HISD888 NE23129   4.108   3.391   3.630   3.562   4.763   3.706   3.230\n HISD893 NE23224   2.060   1.912   1.753   1.983   3.456   2.151   2.308\n  MET908  SD3462   3.928   2.747   1.769   2.463   4.179   2.107   1.670\n  CYS939  SG3932   4.321   3.174   2.232   2.925   4.631   2.597   2.071\n  MET945  SD4028   4.384   3.693   2.561   3.489   5.271   3.236   2.889\n  MET947  SD4064   4.014   2.907   2.096   2.711   4.426   2.454   1.925\n  CYS950  SG4116   3.368   2.551   1.832   2.435   4.163   2.310   1.989\n  MET952  SD4154   4.094   3.464   2.854   3.419   5.066   3.345   2.931\n  MET971  SD4479   3.836   3.087   1.768   2.809   4.605   2.492   2.299\n                 HISD805  CYS818  MET825 HISE835 HISE850 HISD870  MET881\n                 NE21778  SG1989  SD2094 NE22276 NE22524 NE22846  SD3017\n  CYS818  SG1989   1.803\n  MET825  SD2094   2.465   1.251\n HISE835 NE22276   2.481   1.663   0.593\n HISE850 NE22524   1.892   1.588   1.448   1.597\n HISD870 NE22846   4.415   3.189   2.239   2.125   3.622\n  MET881  SD3017   3.085   1.917   1.143   1.081   2.541   1.354\n HISD888 NE23129   4.366   3.052   2.455   2.462   3.898   0.983   1.409\n HISD893 NE23224   3.384   1.999   0.933   1.207   2.071   1.824   1.336\n  MET908  SD3462   1.686   0.517   1.711   2.057   1.984   3.488   2.189\n  CYS939  SG3932   2.082   0.934   2.031   2.388   2.486   3.534   2.294\n  MET945  SD4028   3.071   1.494   2.302   2.796   2.967   3.461   2.492\n  MET947  SD4064   2.260   0.820   1.664   2.028   2.384   3.044   1.827\n  CYS950  SG4116   2.700   0.996   1.115   1.577   2.204   2.388   1.296\n  MET952  SD4154   3.632   1.971   2.049   2.430   3.254   2.308   1.694\n  MET971  SD4479   2.353   0.799   1.845   2.352   2.146   3.564   2.417\n                 HISD888 HISD893  MET908  CYS939  MET945  MET947  CYS950\n                 NE23129 NE23224  SD3462  SG3932  SD4028  SD4064  SG4116\n HISD893 NE23224   2.240\n  MET908  SD3462   3.227   2.469\n  CYS939  SG3932   3.131   2.697   0.518\n  MET945  SD4028   2.985   2.620   1.396   1.079\n  MET947  SD4064   2.661   2.276   0.667   0.493   1.032\n  CYS950  SG4116   2.161   1.486   1.260   1.299   1.268   0.843\n  MET952  SD4154   1.734   2.061   2.064   1.840   1.308   1.439   1.062\n  MET971  SD4479   3.301   2.354   0.817   0.874   0.907   0.926   1.181\n                  MET952\n                  SD4154\n  MET971  SD4479   1.846\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/dna.arn\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/rna.arn\nBefore cleaning: 12511 pairs\nBefore cleaning: 13015 dihedrals\n\nGROMACS reminds you: &amp;quot;Dr Pauling, how do you have so many good ideas? Well David, I have a lot of ideas and throw away the bad ones.&amp;quot; (Linus Pauling)\n\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_107/pdb2gmx/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:203 Ignored file amber99sb-ildn.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:203 Ignored file amber99sb-ildn.ff/spce.itp\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:203 Ignored file amber99sb-ildn.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:149 [&amp;#x27;pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;pdb2gmx_posre.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:150 to: /tmp/biobb/unitests_107/pdb2gmx/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Removed: [&amp;#x27;pdb2gmx_posre.itp&amp;#x27;, &amp;#x27;pdb2gmx_p2g.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_solvate.py::TestSolvate::test_solvate&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_solvate.py::TestSolvate::test_solvate&#34;, &#34;duration&#34;: &#34;782 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_solvate.py::TestSolvate::test_solvate&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;782 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/solvate/output_gro.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_107/solvate/output_gro.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_solvate.gro\nChecking if empty file: /tmp/biobb/unitests_107/solvate/output_top_zip.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_107/solvate/output_top_zip.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_solvate.zip\nComparing TOP/ITP:\n     FILE_A: 40ded017-3ce1-41c1-a556-f9e33dfac48c/A.Lys58Glu_step4_p2g_p2g.itp\n     FILE_B: 858511ea-19d1-4496-bbc8-1630626a0aa6/A.Lys58Glu_step4_p2g_p2g.itp\nComparing TOP/ITP:\n     FILE_A: 40ded017-3ce1-41c1-a556-f9e33dfac48c/A.Lys58Glu_step4_p2g_p2g.top\n     FILE_B: 858511ea-19d1-4496-bbc8-1630626a0aa6/A.Lys58Glu_step4_p2g_p2g.top\n\n------------------------------ Captured log call -------------------------------\nINFO     4fa49d18-101a-408b-9b3f-58c4ad51124f/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     4fa49d18-101a-408b-9b3f-58c4ad51124f/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     4fa49d18-101a-408b-9b3f-58c4ad51124f/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/solvate\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.solvate Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/solvate.gro to /tmp/biobb/unitests_107/solvate/fba7270e-dcdb-4269-b07b-4954d71b7d3c\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/solvate.zip\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:174 [&amp;#x27;fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/solvate.zip\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:256 fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.itp\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:256 fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.top\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright solvate -cp /tmp/biobb/unitests_107/solvate/fba7270e-dcdb-4269-b07b-4954d71b7d3c/solvate.gro -cs spc216.gro -o /tmp/biobb/unitests_107/solvate/fba7270e-dcdb-4269-b07b-4954d71b7d3c/output_gro.gro -p fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.top\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:cmd_wrapper.py:52 \nWARNING: Masses and atomic (Van der Waals) radii will be guessed\n         based on residue and atom names, since they could not be\n         definitively assigned from the information in your input\n         files. These guessed numbers might deviate from the mass\n         and radius of the atom type. Please check the output\n         files if necessary. Note, that this functionality may\n         be removed in a future GROMACS version. Please, consider\n         using another file format for your input.\n\nNOTE: From version 5.0 gmx solvate uses the Van der Waals radii\nfrom the source below. This means the results may be different\ncompared to previous GROMACS versions.\n\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\nA. Bondi\nvan der Waals Volumes and Radii\nJ. Phys. Chem. 68 (1964) pp. 441-451\n-------- -------- --- Thank You --- -------- --------\n\nAdding line for 23502 solvent molecules with resname (SOL) to topology file (fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.top)\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx solvate, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/solvate\nCommand line:\n  gmx -nobackup -nocopyright solvate -cp /tmp/biobb/unitests_107/solvate/fba7270e-dcdb-4269-b07b-4954d71b7d3c/solvate.gro -cs spc216.gro -o /tmp/biobb/unitests_107/solvate/fba7270e-dcdb-4269-b07b-4954d71b7d3c/output_gro.gro -p fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.top\n\nReading solute configuration\nReading solvent configuration\n\nInitialising inter-atomic distances...\nGenerating solvent configuration\nWill generate new solvent configuration of 5x5x5 boxes\nSolvent box contains 80550 atoms in 26850 residues\nRemoved 8835 solvent atoms due to solvent-solvent overlap\nRemoved 1209 solvent atoms due to solute-solvent overlap\nSorting configuration\nFound 1 molecule type:\n    SOL (   3 atoms): 23502 residues\nGenerated solvent containing 70506 atoms in 23502 residues\nWriting generated configuration to /tmp/biobb/unitests_107/solvate/fba7270e-dcdb-4269-b07b-4954d71b7d3c/output_gro.gro\n\nOutput configuration contains 71702 atoms in 23581 residues\nVolume                 :      729.19 (nm^3)\nDensity                :     985.432 (g/l)\nNumber of solvent molecules:  23502   \n\nProcessing topology\n\nGROMACS reminds you: &amp;quot;Here&amp;#x27;s Another Useful Quote&amp;quot; (S. Boot)\n\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_107/solvate/fba7270e-dcdb-4269-b07b-4954d71b7d3c/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:203 Ignored file fd3a06fb-d64f-41e0-8150-dbac98aba625/amber99sb-ildn.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:203 Ignored file fd3a06fb-d64f-41e0-8150-dbac98aba625/amber99sb-ildn.ff/spce.itp\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:203 Ignored file fd3a06fb-d64f-41e0-8150-dbac98aba625/amber99sb-ildn.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:149 [&amp;#x27;fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:150 to: /tmp/biobb/unitests_107/solvate/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:391 Removed: [&amp;#x27;fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;fd3a06fb-d64f-41e0-8150-dbac98aba625/A.Lys58Glu_step4_p2g_p2g.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py::TestSolvate::test_solvate&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py::TestSolvate::test_solvate&#34;, &#34;duration&#34;: &#34;259 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py::TestSolvate::test_solvate&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;259 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/trjcat/output_trjcat.trr\nComparing: \n        File_A: /tmp/biobb/unitests_107/trjcat/output_trjcat.trr\n        File_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_trjcat.trr\n        File_A hash: b&amp;#x27;\\x0f\\xc2\\xe1L\\xf6V&amp;amp;\\x05\\x8e\\xae\\xb5\\xdf\\x9aJD1d\\xf5\\x1bl\\x9b\\xda\\x82Fd\\x96\\xf1)&amp;amp;\\x0f6\\xef&amp;#x27;\n        File_B hash: b&amp;#x27;\\x0f\\xc2\\xe1L\\xf6V&amp;amp;\\x05\\x8e\\xae\\xb5\\xdf\\x9aJD1d\\xf5\\x1bl\\x9b\\xda\\x82Fd\\x96\\xf1)&amp;amp;\\x0f6\\xef&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     39b720a7-a51a-4d5a-b1ce-468b67c3c0b7/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     39b720a7-a51a-4d5a-b1ce-468b67c3c0b7/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     39b720a7-a51a-4d5a-b1ce-468b67c3c0b7/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/trjcat\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.trjcat Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/trjcat.zip\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:174 [&amp;#x27;a0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_a.trr&amp;#x27;, &amp;#x27;a0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_b.trr&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:391 Only concatenate the files without removal of frames with identical timestamps.\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright trjcat -f a0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_a.trr a0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_b.trr -o /tmp/biobb/unitests_107/trjcat/4dfef0de-607e-4843-b639-a7744ac8710b/output_trjcat.trr -cat\n\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:cmd_wrapper.py:52 Note that major changes are planned in future for trjcat, to improve usability and utility.\nlasttime 0\n\nlasttime 30\n\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx trjcat, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/trjcat\nCommand line:\n  gmx -nobackup -nocopyright trjcat -f a0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_a.trr a0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_b.trr -o /tmp/biobb/unitests_107/trjcat/4dfef0de-607e-4843-b639-a7744ac8710b/output_trjcat.trr -cat\n\ntrr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \n\nSummary of files and start times used:\n\n          File                Start time       Time step\n---------------------------------------------------------\na0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_a.trr        0.000 ps       10.000 ps\na0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_b.trr        0.000 ps       10.000 ps WARNING: same Start time as previous\n\n\rReading frame       0 time    0.000   \nContinue writing frames from a0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_a.trr t=0 ps, frame=0      \n -&amp;gt;  frame      0 time    0.000 ps     \r\rReading frame       1 time   10.000    -&amp;gt;  frame      1 time   10.000 ps     \r\rReading frame       2 time   20.000    -&amp;gt;  frame      2 time   20.000 ps     \r\rReading frame       3 time   30.000    -&amp;gt;  frame      3 time   30.000 ps     \r\rLast frame          3 time   30.000   \n\rReading frame       0 time    0.000   \nContinue writing frames from a0135f9f-50bf-488a-b343-3d2b6414d02b/ref_trjcat_b.trr t=0 ps, frame=4      \n -&amp;gt;  frame      4 time    0.000 ps     \r\rReading frame       1 time   10.000    -&amp;gt;  frame      5 time   10.000 ps     \r\rReading frame       2 time   20.000    -&amp;gt;  frame      6 time   20.000 ps     \r\rReading frame       3 time   30.000    -&amp;gt;  frame      7 time   30.000 ps     \r\rLast frame          3 time   30.000   \n\nLast frame written was 7, time 30.000000 ps\n\nGROMACS reminds you: &amp;quot;Therefore, things must be learned only to be unlearned again or, more likely, to be corrected.&amp;quot; (Richard Feynman)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py::TestAppendLigand::test_append_ligand&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py::TestAppendLigand::test_append_ligand&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py::TestAppendLigand::test_append_ligand&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/append_ligand/output_top_zip.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_107/append_ligand/output_top_zip.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs_extra/ref_appendligand.zip\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/append_ligand_ligand.top\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/append_ligand_ligand.top\nComparing TOP/ITP:\n     FILE_A: c4e55ad1-eff9-4e1e-92e3-1300c48dfe8c/pep_ligand.itp\n     FILE_B: 58c5956d-284d-46e7-a54e-c83dacadcb7b/pep_ligand.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs_extra.append_ligand Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:174 [&amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step8_gio_gio.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step8_gio_gio.top\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_107/append_ligand/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:203 Ignored file 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/amber99sb.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:203 Ignored file 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/posre_PEP-H.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:203 Ignored file 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/amber99sb.ff/tip3p.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:203 Ignored file 4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/amber99sb.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:149 [&amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/append_ligand_ligand.top&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/pep_ligand.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:150 to: /tmp/biobb/unitests_107/append_ligand/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:391 Removed: [&amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/pep_ligand.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27;, &amp;#x27;4cc9fbb8-ff8f-4f55-9ee5-1a6ed026a2c2/append_ligand_ligand.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py::TestNdx2resttop::test_ndx2resttop&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py::TestNdx2resttop::test_ndx2resttop&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py::TestNdx2resttop::test_ndx2resttop&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/ndx2resttop/output_top_zip.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_107/ndx2resttop/output_top_zip.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs_extra/ref_ndx2resttop.zip\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ALL.Ala115Pro_step8_gio_gio.top\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ALL.Ala115Pro_step8_gio_gio.top\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ndx2resttop_Chain_A_noMut.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ndx2resttop_Chain_A_noMut.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ndx2resttop_Chain_B_noMut.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ndx2resttop_Chain_B_noMut.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ndx2resttop_Chain_C_noMut.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ndx2resttop_Chain_C_noMut.itp\nComparing TOP/ITP:\n     FILE_A: b3908998-ec8d-4715-bda3-91534bdc2dc2/ndx2resttop_Chain_D_noMut.itp\n     FILE_B: d82d0e2a-7aa6-4eba-ad96-599b6a7cc07d/ndx2resttop_Chain_D_noMut.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs_extra.ndx2resttop Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:174 [&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step8_gio_gio.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step8_gio_gio.top\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Index_dic: {&amp;#x27;[ System ]&amp;#x27;: (0,), &amp;#x27;[ Protein ]&amp;#x27;: (26363, 26363), &amp;#x27;[ Protein-H ]&amp;#x27;: (28474, 28474), &amp;#x27;[ C-alpha ]&amp;#x27;: (29520, 29520), &amp;#x27;[ Backbone ]&amp;#x27;: (29659, 29659), &amp;#x27;[ MainChain ]&amp;#x27;: (30074, 30074), &amp;#x27;[ MainChain+Cb ]&amp;#x27;: (30627, 30627), &amp;#x27;[ MainChain+H ]&amp;#x27;: (31306, 31306), &amp;#x27;[ SideChain ]&amp;#x27;: (31990, 31990), &amp;#x27;[ SideChain-H ]&amp;#x27;: (33418, 33418), &amp;#x27;[ Prot-Masses ]&amp;#x27;: (33912, 33912), &amp;#x27;[ non-Protein ]&amp;#x27;: (36023, 36023), &amp;#x27;[ Water ]&amp;#x27;: (60276, 60276), &amp;#x27;[ SOL ]&amp;#x27;: (84512, 84512), &amp;#x27;[ non-Water ]&amp;#x27;: (108748, 108748), &amp;#x27;[ Ion ]&amp;#x27;: (110876, 110876), &amp;#x27;[ NA ]&amp;#x27;: (110894, 110894), &amp;#x27;[ CL ]&amp;#x27;: (110904, 110904), &amp;#x27;[ Water_and_ions ]&amp;#x27;: (110914, 110914), &amp;#x27;[ Chain_A ]&amp;#x27;: (135167, 135167), &amp;#x27;[ Chain_B ]&amp;#x27;: (135696, 135696), &amp;#x27;[ Chain_C ]&amp;#x27;: (136225, 136225), &amp;#x27;[ Chain_D ]&amp;#x27;: (136754, 136754), &amp;#x27;[ Chain_A_noMut ]&amp;#x27;: (137283, 137283), &amp;#x27;[ Chain_B_noMut ]&amp;#x27;: (137545, 137545), &amp;#x27;[ Chain_C_noMut ]&amp;#x27;: (137807, 137807), &amp;#x27;[ Chain_D_noMut ]&amp;#x27;: (138069, 138069), &amp;#x27;[ Chain_A_backbone ]&amp;#x27;: (138331, 138331), &amp;#x27;[ Chain_B_backbone ]&amp;#x27;: (138470, 138470), &amp;#x27;[ Chain_C_backbone ]&amp;#x27;: (138609, 138609), &amp;#x27;[ Chain_D_backbone ]&amp;#x27;: (138748, 138748), &amp;#x27;[ Chain_all_noMut ]&amp;#x27;: (138887, 138887), &amp;#x27;[ Chain_all_backbone ]&amp;#x27;: (139932, 139932), &amp;#x27;[ Chain_A_Heavy ]&amp;#x27;: (140485, 140485), &amp;#x27;[ Chain_B_Heavy ]&amp;#x27;: (140748, 140748), &amp;#x27;[ Chain_C_Heavy ]&amp;#x27;: (141011, 141011), &amp;#x27;[ Chain_D_Heavy ]&amp;#x27;: (141274, 141536)}\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 ref_rest_chain_triplet_list: [(&amp;#x27;Chain_A&amp;#x27;, &amp;#x27;Chain_A_noMut&amp;#x27;, &amp;#x27;A&amp;#x27;), (&amp;#x27;Chain_B&amp;#x27;, &amp;#x27;Chain_B_noMut&amp;#x27;, &amp;#x27;B&amp;#x27;), (&amp;#x27;Chain_C&amp;#x27;, &amp;#x27;Chain_C_noMut&amp;#x27;, &amp;#x27;C&amp;#x27;), (&amp;#x27;Chain_D&amp;#x27;, &amp;#x27;Chain_D_noMut&amp;#x27;, &amp;#x27;D&amp;#x27;)]\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Reference group: Chain_A\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Restrain group: Chain_A_noMut\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Chain: A\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 reference_group_index: start_closed:135168 stop_open: 135167\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 restrain_group_index: start_closed:137284 stop_open: 137283\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Creating: &amp;lt;_io.TextIOWrapper name=&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ndx2resttop_Chain_A_noMut.itp&amp;#x27; mode=&amp;#x27;w&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the selected atoms force constants\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Opening: &amp;lt;_io.TextIOWrapper name=&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27; mode=&amp;#x27;a&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the ifdef include statement\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Reference group: Chain_B\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Restrain group: Chain_B_noMut\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Chain: B\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 reference_group_index: start_closed:135697 stop_open: 135696\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 restrain_group_index: start_closed:137546 stop_open: 137545\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Creating: &amp;lt;_io.TextIOWrapper name=&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ndx2resttop_Chain_B_noMut.itp&amp;#x27; mode=&amp;#x27;w&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the selected atoms force constants\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Opening: &amp;lt;_io.TextIOWrapper name=&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27; mode=&amp;#x27;a&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the ifdef include statement\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Reference group: Chain_C\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Restrain group: Chain_C_noMut\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Chain: C\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 reference_group_index: start_closed:136226 stop_open: 136225\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 restrain_group_index: start_closed:137808 stop_open: 137807\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Creating: &amp;lt;_io.TextIOWrapper name=&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ndx2resttop_Chain_C_noMut.itp&amp;#x27; mode=&amp;#x27;w&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the selected atoms force constants\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Opening: &amp;lt;_io.TextIOWrapper name=&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27; mode=&amp;#x27;a&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the ifdef include statement\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Reference group: Chain_D\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Restrain group: Chain_D_noMut\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Chain: D\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 reference_group_index: start_closed:136755 stop_open: 136754\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 restrain_group_index: start_closed:138070 stop_open: 138069\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Creating: &amp;lt;_io.TextIOWrapper name=&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ndx2resttop_Chain_D_noMut.itp&amp;#x27; mode=&amp;#x27;w&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the selected atoms force constants\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Opening: &amp;lt;_io.TextIOWrapper name=&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27; mode=&amp;#x27;a&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the ifdef include statement\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:203 Ignored file cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/amber99sb.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:203 Ignored file cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/amber99sb.ff/tip3p.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:203 Ignored file cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/amber99sb.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:149 [&amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;cf8ec31c-3c90-40bc-a1e4-3bd7c60a8652/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, 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+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.8.19&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.10&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.1&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_gromacs/test/unitests/test_gromacs/test_editconf.py::TestEditconf::test_editconf&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_editconf.py::TestEditconf::test_editconf&#34;, &#34;duration&#34;: &#34;106 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_editconf.py::TestEditconf::test_editconf&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;106 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/editconf/output_gro.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_107/editconf/output_gro.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_editconf.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     50339931-8bf4-47b2-b8ac-1584e3fd3293/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     50339931-8bf4-47b2-b8ac-1584e3fd3293/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     50339931-8bf4-47b2-b8ac-1584e3fd3293/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/editconf\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.editconf Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/editconf.gro to /tmp/biobb/unitests_107/editconf/f593ff51-a981-465a-93ae-eb1c725625ee\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Distance of the box to molecule:   1.00\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Centering molecule in the box.\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:file_utils.py:391 Box type: cubic\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright editconf -f /tmp/biobb/unitests_107/editconf/f593ff51-a981-465a-93ae-eb1c725625ee/editconf.gro -o /tmp/biobb/unitests_107/editconf/f593ff51-a981-465a-93ae-eb1c725625ee/output_gro.gro -bt cubic -d 1.0 -c\n\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.out:cmd_wrapper.py:52 Note that major changes are planned in future for editconf, to improve usability and utility.\nRead 1196 atoms\nVolume: 729.19 nm^3, corresponds to roughly 328100 electrons\nNo velocities found\n    system size :  5.722  6.526  3.712 (nm)\n    diameter    :  7.001               (nm)\n    center      :  4.500  4.501  4.501 (nm)\n    box vectors :  9.001  9.001  9.001 (nm)\n    box angles  :  90.00  90.00  90.00 (degrees)\n    box volume  : 729.19               (nm^3)\n    shift       :  0.000 -0.000 -0.000 (nm)\nnew center      :  4.500  4.500  4.500 (nm)\nnew box vectors :  9.001  9.001  9.001 (nm)\nnew box angles  :  90.00  90.00  90.00 (degrees)\nnew box volume  : 729.19               (nm^3)\n\nINFO     /tmp/biobb/unitests_107/editconf/editconf_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx editconf, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/editconf\nCommand line:\n  gmx -nobackup -nocopyright editconf -f /tmp/biobb/unitests_107/editconf/f593ff51-a981-465a-93ae-eb1c725625ee/editconf.gro -o /tmp/biobb/unitests_107/editconf/f593ff51-a981-465a-93ae-eb1c725625ee/output_gro.gro -bt cubic -d 1.0 -c\n\n\nGROMACS reminds you: &amp;quot;I Calculate My Birthright&amp;quot; (P.J. Harvey)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_genion.py::TestGenion::test_genion&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_genion.py::TestGenion::test_genion&#34;, &#34;duration&#34;: &#34;207 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_genion.py::TestGenion::test_genion&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;207 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/genion/output_gro.gro\nChecking if empty file: /tmp/biobb/unitests_107/genion/output_top_zip.zip\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_107/genion/output_gro.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_genion.gro\n     SIZE_A: 3222684 bytes\n     SIZE_B: 3222684 bytes\n     TOLERANCE: 1.0%, Low: 3190457.16 bytes, High: 3254910.84 bytes\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_107/genion/output_top_zip.zip\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_genion.zip\n     SIZE_A: 375866 bytes\n     SIZE_B: 375866 bytes\n     TOLERANCE: 1.0%, Low: 372107.34 bytes, High: 379624.66 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     afcd4068-1ac8-4e82-a6b5-1c9d714190bc/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     afcd4068-1ac8-4e82-a6b5-1c9d714190bc/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     afcd4068-1ac8-4e82-a6b5-1c9d714190bc/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genion\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.genion Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genion.tpr to /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/genion/4387fb81-f69d-4ea4-a8db-a3b9f4e0c5a2.stdin to /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genion.zip\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:174 [&amp;#x27;f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step8_gio_gio.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genion.zip\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:256 f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step4_p2g_p2g.itp\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:256 f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step8_gio_gio.top\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 To reach up 0.05 mol/litre concentration\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright genion -s /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300/genion.tpr -o /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300/output_gro.gro -p f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step8_gio_gio.top -conc 0.05 -seed 1993 &amp;lt; /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300/4387fb81-f69d-4ea4-a8db-a3b9f4e0c5a2.stdin\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:cmd_wrapper.py:52 Will try to add 22 NA ions and 22 CL ions.\nSelect a continuous group of solvent molecules\nSelected 13: &amp;#x27;SOL&amp;#x27;\n\nProcessing topology\nReplacing 44 solute molecules in topology file (f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step8_gio_gio.top)  by 22 NA and 22 CL ions.\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx genion, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genion\nCommand line:\n  gmx -nobackup -nocopyright genion -s /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300/genion.tpr -o /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300/output_gro.gro -p f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step8_gio_gio.top -conc 0.05 -seed 1993\n\nReading file /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300/genion.tpr, VERSION 5.1.2 (single precision)\nReading file /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300/genion.tpr, VERSION 5.1.2 (single precision)\nGroup     0 (         System) has 71702 elements\nGroup     1 (        Protein) has  1196 elements\nGroup     2 (      Protein-H) has   618 elements\nGroup     3 (        C-alpha) has    79 elements\nGroup     4 (       Backbone) has   237 elements\nGroup     5 (      MainChain) has   317 elements\nGroup     6 (   MainChain+Cb) has   393 elements\nGroup     7 (    MainChain+H) has   396 elements\nGroup     8 (      SideChain) has   800 elements\nGroup     9 (    SideChain-H) has   301 elements\nGroup    10 (    Prot-Masses) has  1196 elements\nGroup    11 (    non-Protein) has 70506 elements\nGroup    12 (          Water) has 70506 elements\nGroup    13 (            SOL) has 70506 elements\nGroup    14 (      non-Water) has  1196 elements\nSelect a group: Number of (3-atomic) solvent molecules: 23502\nUsing random seed 1993.\nReplacing solvent molecule 8233 (atom 25895) with NA\nReplacing solvent molecule 1966 (atom 7094) with NA\nReplacing solvent molecule 5861 (atom 18779) with NA\nReplacing solvent molecule 3984 (atom 13148) with NA\nReplacing solvent molecule 17732 (atom 54392) with NA\nReplacing solvent molecule 12114 (atom 37538) with NA\nReplacing solvent molecule 19279 (atom 59033) with NA\nReplacing solvent molecule 13218 (atom 40850) with NA\nReplacing solvent molecule 15841 (atom 48719) with NA\nReplacing solvent molecule 7583 (atom 23945) with NA\nReplacing solvent molecule 13527 (atom 41777) with NA\nReplacing solvent molecule 16709 (atom 51323) with NA\nReplacing solvent molecule 1660 (atom 6176) with NA\nReplacing solvent molecule 14850 (atom 45746) with NA\nReplacing solvent molecule 5431 (atom 17489) with NA\nReplacing solvent molecule 20277 (atom 62027) with NA\nReplacing solvent molecule 9374 (atom 29318) with NA\nReplacing solvent molecule 4205 (atom 13811) with NA\nReplacing solvent molecule 15329 (atom 47183) with NA\nReplacing solvent molecule 208 (atom 1820) with NA\nReplacing solvent molecule 4341 (atom 14219) with NA\nReplacing solvent molecule 14344 (atom 44228) with NA\nReplacing solvent molecule 12731 (atom 39389) with CL\nReplacing solvent molecule 2246 (atom 7934) with CL\nReplacing solvent molecule 10972 (atom 34112) with CL\nReplacing solvent molecule 1350 (atom 5246) with CL\nReplacing solvent molecule 11157 (atom 34667) with CL\nReplacing solvent molecule 15670 (atom 48206) with CL\nReplacing solvent molecule 7900 (atom 24896) with CL\nReplacing solvent molecule 12147 (atom 37637) with CL\nReplacing solvent molecule 3049 (atom 10343) with CL\nReplacing solvent molecule 15083 (atom 46445) with CL\nReplacing solvent molecule 16474 (atom 50618) with CL\nReplacing solvent molecule 21986 (atom 67154) with CL\nReplacing solvent molecule 12088 (atom 37460) with CL\nReplacing solvent molecule 5004 (atom 16208) with CL\nReplacing solvent molecule 14621 (atom 45059) with CL\nReplacing solvent molecule 8784 (atom 27548) with CL\nReplacing solvent molecule 20066 (atom 61394) with CL\nReplacing solvent molecule 13479 (atom 41633) with CL\nReplacing solvent molecule 22247 (atom 67937) with CL\nReplacing solvent molecule 11017 (atom 34247) with CL\nReplacing solvent molecule 14301 (atom 44099) with CL\nReplacing solvent molecule 6548 (atom 20840) with CL\n\n\nGROMACS reminds you: &amp;quot;I Calculate My Birthright&amp;quot; (P.J. Harvey)\n\n\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_107/genion/b193b684-4703-42f4-b6ad-5d75bae79300/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:203 Ignored file f88242ee-4b97-454c-8894-afdcbac97c21/amber99sb-ildn.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:203 Ignored file f88242ee-4b97-454c-8894-afdcbac97c21/amber99sb-ildn.ff/spce.itp\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:203 Ignored file f88242ee-4b97-454c-8894-afdcbac97c21/amber99sb-ildn.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:149 [&amp;#x27;f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step8_gio_gio.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:150 to: /tmp/biobb/unitests_107/genion/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/genion/genion_log.out:file_utils.py:391 Removed: [&amp;#x27;f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;f88242ee-4b97-454c-8894-afdcbac97c21/A.Lys58Glu_step8_gio_gio.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr&#34;, &#34;duration&#34;: &#34;542 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;542 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/genrestr/output_itp.itp\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_107/genrestr/output_itp.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_genrestr.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     3f25725c-0749-454b-af32-63a9183924e0/log.out:cmd_wrapper.py:33 gmx  -nobackup -nocopyright -version\n\nINFO     3f25725c-0749-454b-af32-63a9183924e0/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     3f25725c-0749-454b-af32-63a9183924e0/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genrestr\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.genrestr Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genrestr.gro to /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genrestr.ndx to /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/genrestr/11beca7d-c49d-4a12-a784-e5fb59506bce.stdin to /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:cmd_wrapper.py:33 gmx  -nobackup -nocopyright genrestr -f /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09/genrestr.gro -o /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09/output_itp.itp -fc 500 500 500 -n /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09/genrestr.ndx &amp;lt; /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09/11beca7d-c49d-4a12-a784-e5fb59506bce.stdin\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.out:cmd_wrapper.py:52 Select group to position restrain\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx genrestr, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genrestr\nCommand line:\n  gmx -nobackup -nocopyright genrestr -f /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09/genrestr.gro -o /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09/output_itp.itp -fc 500 500 500 -n /tmp/biobb/unitests_107/genrestr/308a8ae2-e200-4162-9380-4754187d3c09/genrestr.ndx\n\n\nReading structure file\nGroup     0 (         System) has 31633 elements\nGroup     1 (        Protein) has 31633 elements\nGroup     2 (      Protein-H) has 15652 elements\nGroup     3 (        C-alpha) has  2068 elements\nGroup     4 (       Backbone) has  6204 elements\nGroup     5 (      MainChain) has  8276 elements\nGroup     6 (   MainChain+Cb) has 10164 elements\nGroup     7 (    MainChain+H) has 10248 elements\nGroup     8 (      SideChain) has 21385 elements\nGroup     9 (    SideChain-H) has  7376 elements\nGroup    10 (    chA_&amp;amp;_r_513) has    20 elements\nGroup    11 (    chB_&amp;amp;_r_513) has    20 elements\nSelect a group: \nGROMACS reminds you: &amp;quot;The World is a Friendly Place&amp;quot; (Magnapop)\n\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr_noNDX&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr_noNDX&#34;, &#34;duration&#34;: &#34;874 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_genrestr.py::TestGenrestr::test_genrestr_noNDX&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;874 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/genrestr/output_itp.itp\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_107/genrestr/output_itp.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_genrestr_noNDX.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     e64cdb5c-fb6b-4086-aa61-5b8eb6eab5cc/log.out:cmd_wrapper.py:33 gmx  -nobackup -nocopyright -version\n\nINFO     e64cdb5c-fb6b-4086-aa61-5b8eb6eab5cc/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     e64cdb5c-fb6b-4086-aa61-5b8eb6eab5cc/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genrestr\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:file_utils.py:391 Executing biobb_gromacs.gromacs.genrestr Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/genrestr.gro to /tmp/biobb/unitests_107/genrestr/a328c752-3fdf-48ae-8997-e24c4e3fce4d\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/genrestr/16876555-5c42-4175-8165-a9068a6db7bd.stdin to /tmp/biobb/unitests_107/genrestr/a328c752-3fdf-48ae-8997-e24c4e3fce4d\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:cmd_wrapper.py:33 gmx  -nobackup -nocopyright genrestr -f /tmp/biobb/unitests_107/genrestr/a328c752-3fdf-48ae-8997-e24c4e3fce4d/genrestr.gro -o /tmp/biobb/unitests_107/genrestr/a328c752-3fdf-48ae-8997-e24c4e3fce4d/output_itp.itp -fc 500 500 500 &amp;lt; /tmp/biobb/unitests_107/genrestr/a328c752-3fdf-48ae-8997-e24c4e3fce4d/16876555-5c42-4175-8165-a9068a6db7bd.stdin\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.out:cmd_wrapper.py:52 Select group to position restrain\nSelected 0: &amp;#x27;System&amp;#x27;\n\nINFO     /tmp/biobb/unitests_107/genrestr/genrestr_log1.err:cmd_wrapper.py:60                :-) GROMACS - gmx genrestr, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/genrestr\nCommand line:\n  gmx -nobackup -nocopyright genrestr -f /tmp/biobb/unitests_107/genrestr/a328c752-3fdf-48ae-8997-e24c4e3fce4d/genrestr.gro -o /tmp/biobb/unitests_107/genrestr/a328c752-3fdf-48ae-8997-e24c4e3fce4d/output_itp.itp -fc 500 500 500\n\n\nReading structure file\nGroup     0 (         System) has 71690 elements\nGroup     1 (        Protein) has  1196 elements\nGroup     2 (      Protein-H) has   618 elements\nGroup     3 (        C-alpha) has    79 elements\nGroup     4 (       Backbone) has   237 elements\nGroup     5 (      MainChain) has   317 elements\nGroup     6 (   MainChain+Cb) has   393 elements\nGroup     7 (    MainChain+H) has   396 elements\nGroup     8 (      SideChain) has   800 elements\nGroup     9 (    SideChain-H) has   301 elements\nGroup    10 (    Prot-Masses) has  1196 elements\nGroup    11 (    non-Protein) has 70494 elements\nGroup    12 (          Water) has 70488 elements\nGroup    13 (            SOL) has 70488 elements\nGroup    14 (      non-Water) has  1202 elements\nGroup    15 (            Ion) has     6 elements\nGroup    16 (             NA) has     6 elements\nGroup    17 ( Water_and_ions) has 70494 elements\nSelect a group: \nGROMACS reminds you: &amp;quot;The World is a Friendly Place&amp;quot; (Magnapop)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py::TestGmxselect::test_select&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py::TestGmxselect::test_select&#34;, &#34;duration&#34;: &#34;244 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_gmxselect.py::TestGmxselect::test_select&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;244 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/gmxselect/output_ndx.ndx\nComparing: \n        File_A: /tmp/biobb/unitests_107/gmxselect/output_ndx.ndx\n        File_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_select.ndx\n        File_A hash: b&amp;#x27;^v&amp;gt;\\xac\\x07\\xf2\\tpB+\\xc57\\xf9X\\xc8\\xd3\\xb6\\xaf\\xfb{\\x18@\\xe7\\x8e\\xaeF\\x00b\\xea\\xc8\\x19$&amp;#x27;\n        File_B hash: b&amp;#x27;^v&amp;gt;\\xac\\x07\\xf2\\tpB+\\xc57\\xf9X\\xc8\\xd3\\xb6\\xaf\\xfb{\\x18@\\xe7\\x8e\\xaeF\\x00b\\xea\\xc8\\x19$&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     0db26a0d-189c-4269-90f7-16ee03d5dc3c/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     0db26a0d-189c-4269-90f7-16ee03d5dc3c/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     0db26a0d-189c-4269-90f7-16ee03d5dc3c/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/gmxselect\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.gmxselect Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/make_ndx.tpr to /tmp/biobb/unitests_107/gmxselect/bb292a84-d924-4f48-a63b-54ecd8e02dbc\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright select -s /tmp/biobb/unitests_107/gmxselect/bb292a84-d924-4f48-a63b-54ecd8e02dbc/make_ndx.tpr -on /tmp/biobb/unitests_107/gmxselect/bb292a84-d924-4f48-a63b-54ecd8e02dbc/output_ndx.ndx -select &amp;#x27;&amp;quot;Mynewgroup&amp;quot; group &amp;quot;Protein-H&amp;quot; and not same residue as within 0.4 of resname ARG&amp;#x27;\n\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/gmxselect/gmxselect_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx select, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/gmxselect\nCommand line:\n  gmx -nobackup -nocopyright select -s /tmp/biobb/unitests_107/gmxselect/bb292a84-d924-4f48-a63b-54ecd8e02dbc/make_ndx.tpr -on /tmp/biobb/unitests_107/gmxselect/bb292a84-d924-4f48-a63b-54ecd8e02dbc/output_ndx.ndx -select &amp;#x27;&amp;quot;Mynewgroup&amp;quot; group &amp;quot;Protein-H&amp;quot; and not same residue as within 0.4 of resname ARG&amp;#x27;\n\nReading file /tmp/biobb/unitests_107/gmxselect/bb292a84-d924-4f48-a63b-54ecd8e02dbc/make_ndx.tpr, VERSION 5.1.2 (single precision)\nReading file /tmp/biobb/unitests_107/gmxselect/bb292a84-d924-4f48-a63b-54ecd8e02dbc/make_ndx.tpr, VERSION 5.1.2 (single precision)\nAnalyzed topology coordinates\n\nGROMACS reminds you: &amp;quot;Never measure the height of a mountain until you have reached the top. Then you will see how low it was.&amp;quot; (Dag Hammarskjold)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_grompp.py::TestGrompp::test_grompp&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_grompp.py::TestGrompp::test_grompp&#34;, &#34;duration&#34;: &#34;510 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_grompp.py::TestGrompp::test_grompp&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;510 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/grompp/output_tpr.tpr\nComparing GROMACS files:\nFILE_A: /tmp/biobb/unitests_107/grompp/output_tpr.tpr\nFILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr\n\ncmd_wrapper commnand print: gmx check -s1 /tmp/biobb/unitests_107/grompp/output_tpr.tpr -s2 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr &amp;gt; check_result.out\nExit, code 0\nResult file: /tmp/biobb/unitests_107/grompp/check_result.out\n\n------------------------------ Captured log call -------------------------------\nINFO     59bbc2d1-acbb-472d-a873-271f07922cba/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     59bbc2d1-acbb-472d-a873-271f07922cba/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     59bbc2d1-acbb-472d-a873-271f07922cba/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.grompp Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.gro to /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.zip\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:174 [&amp;#x27;/tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/A.Lys58Glu_step6_sol_sol.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.zip\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:256 /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/A.Lys58Glu_step4_p2g_p2g.itp\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:file_utils.py:256 /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/A.Lys58Glu_step6_sol_sol.top\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright grompp -f /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/grompp.mdp -c /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/grompp.gro -r /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/grompp.gro -p /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/A.Lys58Glu_step6_sol_sol.top -o /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/output_tpr.tpr -po mdout.mdp -maxwarn 1\n\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.out:cmd_wrapper.py:52 Generated 2145 of the 2145 non-bonded parameter combinations\n\nGenerated 2145 of the 2145 1-4 parameter combinations\n\nExcluding 3 bonded neighbours molecule type &amp;#x27;Protein_chain_A&amp;#x27;\n\nExcluding 2 bonded neighbours molecule type &amp;#x27;SOL&amp;#x27;\n\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\nJ. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof\nQuantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net\nCharge\nJ. Chem. Theory Comput. 10 (2014) pp. 381-393\n-------- -------- --- Thank You --- -------- --------\n\nAnalysing residue names:\nThere are:    79    Protein residues\nThere are: 23502      Water residues\nAnalysing Protein...\n\nThe largest distance between excluded atoms is 0.417 nm\nCalculating fourier grid dimensions for X Y Z\nUsing a fourier grid of 80x80x80, spacing 0.113 0.113 0.113\n\nEstimate for the relative computational load of the PME mesh part: 0.23\n\nThis run will generate roughly 5 Mb of data\n\nINFO     /tmp/biobb/unitests_107/grompp/grompp_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx grompp, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp\nCommand line:\n  gmx -nobackup -nocopyright grompp -f /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/grompp.mdp -c /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/grompp.gro -r /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/grompp.gro -p /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/A.Lys58Glu_step6_sol_sol.top -o /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/output_tpr.tpr -po mdout.mdp -maxwarn 1\n\nIgnoring obsolete mdp entry &amp;#x27;ns-type&amp;#x27;\nGenerating 1-4 interactions: fudge = 0.5\n\nNOTE 1 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  System has non-zero total charge: -6.000000\n  Total charge should normally be an integer. See\n  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n  for discussion on how close it should be to an integer.\n  \n\n\n\nWARNING 1 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  You are using Ewald electrostatics in a system with net charge. This can\n  lead to severe artifacts, such as ions moving into regions with low\n  dielectric, due to the uniform background charge. We suggest to\n  neutralize your system with counter ions, possibly in combination with a\n  physiological salt concentration.\n\n\nNOTE 2 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  The bond in molecule-type Protein_chain_A between atoms 10 OG and 11 HG\n  has an estimated oscillational period of 9.0e-03 ps, which is less than\n  10 times the time step of 1.0e-03 ps.\n  Maybe you forgot to change the constraints mdp option.\n\nNumber of degrees of freedom in T-Coupling group rest is 144597.00\n\nNOTE 3 [file /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/grompp.mdp]:\n  NVE simulation with an initial temperature of zero: will use a Verlet\n  buffer of 10%. Check your energy drift!\n\n\nNOTE 4 [file /tmp/biobb/unitests_107/grompp/0d9b5cfa-3cdb-41db-b6e9-374230b2cb1c/grompp.mdp]:\n  Removing center of mass motion in the presence of position restraints\n  might cause artifacts. When you are using position restraints to\n  equilibrate a macro-molecule, the artifacts are usually negligible.\n\n\nThere were 4 notes\n\nThere was 1 warning\n\nGROMACS reminds you: &amp;quot;Never measure the height of a mountain until you have reached the top. Then you will see how low it was.&amp;quot; (Dag Hammarskjold)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py::TestGromppMdrun::test_grompp_mdrun&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py::TestGromppMdrun::test_grompp_mdrun&#34;, &#34;duration&#34;: &#34;00:01:09&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_grompp_mdrun.py::TestGromppMdrun::test_grompp_mdrun&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:09&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/grompp_mdrun/output_trr_path.trr\nComparing GROMACS files:\nFILE_A: /tmp/biobb/unitests_107/grompp_mdrun/output_trr_path.trr\nFILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_grompp_mdrun.trr\n\ncmd_wrapper commnand print: echo &amp;quot;Protein Protein&amp;quot; | gmx rms -s /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.gro -f /tmp/biobb/unitests_107/grompp_mdrun/output_trr_path.trr -f2 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_grompp_mdrun.trr -xvg none\nExit, code 0\nResult file: /tmp/biobb/unitests_107/grompp_mdrun/rmsd.xvg\nChecking if empty file: /tmp/biobb/unitests_107/grompp_mdrun/output_gro_path.gro\nChecking if empty file: /tmp/biobb/unitests_107/grompp_mdrun/output_edr_path.edr\nChecking if empty file: /tmp/biobb/unitests_107/grompp_mdrun/output_log_path.log\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log.out:file_utils.py:391 Calling Grompp class\nINFO     d0fa977f-51b6-4449-911c-27200f68ec76/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     d0fa977f-51b6-4449-911c-27200f68ec76/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     d0fa977f-51b6-4449-911c-27200f68ec76/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp_mdrun\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:391 Executing biobb_gromacs.gromacs.grompp Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.gro to /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.zip\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:174 [&amp;#x27;/tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/A.Lys58Glu_step6_sol_sol.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/grompp.zip\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:256 /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/A.Lys58Glu_step4_p2g_p2g.itp\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:file_utils.py:256 /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/A.Lys58Glu_step6_sol_sol.top\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright grompp -f /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/grompp.mdp -c /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/grompp.gro -r /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/grompp.gro -p /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/A.Lys58Glu_step6_sol_sol.top -o /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/internal.tpr -po mdout.mdp -maxwarn 1\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.out:cmd_wrapper.py:52 Generated 2145 of the 2145 non-bonded parameter combinations\n\nGenerated 2145 of the 2145 1-4 parameter combinations\n\nExcluding 3 bonded neighbours molecule type &amp;#x27;Protein_chain_A&amp;#x27;\n\nturning H bonds into constraints...\n\nExcluding 2 bonded neighbours molecule type &amp;#x27;SOL&amp;#x27;\n\nturning H bonds into constraints...\n\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\nJ. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof\nQuantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net\nCharge\nJ. Chem. Theory Comput. 10 (2014) pp. 381-393\n-------- -------- --- Thank You --- -------- --------\n\nAnalysing residue names:\nThere are:    79    Protein residues\nThere are: 23502      Water residues\nAnalysing Protein...\n\nThe largest distance between excluded atoms is 0.417 nm\n\nDetermining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K\n\nCalculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm\n\nSet rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm\n\nNote that mdrun will redetermine rlist based on the actual pair-list setup\nCalculating fourier grid dimensions for X Y Z\nUsing a fourier grid of 80x80x80, spacing 0.113 0.113 0.113\n\nEstimate for the relative computational load of the PME mesh part: 0.27\n\nThis run will generate roughly 11 Mb of data\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log1.err:cmd_wrapper.py:60                 :-) GROMACS - gmx grompp, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp_mdrun\nCommand line:\n  gmx -nobackup -nocopyright grompp -f /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/grompp.mdp -c /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/grompp.gro -r /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/grompp.gro -p /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/A.Lys58Glu_step6_sol_sol.top -o /tmp/biobb/unitests_107/grompp_mdrun/31de74d0-4de2-4e86-815e-2e4e05681597/internal.tpr -po mdout.mdp -maxwarn 1\n\nIgnoring obsolete mdp entry &amp;#x27;ns-type&amp;#x27;\nGenerating 1-4 interactions: fudge = 0.5\n\nNOTE 1 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  System has non-zero total charge: -6.000000\n  Total charge should normally be an integer. See\n  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n  for discussion on how close it should be to an integer.\n  \n\n\n\nWARNING 1 [file A.Lys58Glu_step6_sol_sol.top, line 11402]:\n  You are using Ewald electrostatics in a system with net charge. This can\n  lead to severe artifacts, such as ions moving into regions with low\n  dielectric, due to the uniform background charge. We suggest to\n  neutralize your system with counter ions, possibly in combination with a\n  physiological salt concentration.\n\nNumber of degrees of freedom in T-Coupling group Protein is 3009.94\nNumber of degrees of freedom in T-Coupling group non-Protein is 141009.06\n\nThere was 1 note\n\nThere was 1 warning\n\nGROMACS reminds you: &amp;quot;We think there is color, we think there is sweet, we think there is bitter, but in reality there are atoms and a void.&amp;quot; (Democritus)\n\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log.out:file_utils.py:391 Grompp return code: 0\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log.out:file_utils.py:391 Grompp return code is correct. Calling MDRun class\nINFO     1cf8d964-543c-4273-a246-141a692d3606/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     1cf8d964-543c-4273-a246-141a692d3606/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     1cf8d964-543c-4273-a246-141a692d3606/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp_mdrun\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:file_utils.py:391 Executing biobb_gromacs.gromacs.mdrun Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:file_utils.py:391 Copy: b5b9c140-153c-40ab-a4d9-e38e95e80fc2/internal.tpr to /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:file_utils.py:391 User added number of gmx threads: 0\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright mdrun -o /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/output_trr_path.trr -s /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/internal.tpr -c /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/output_gro_path.gro -e /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/output_edr_path.edr -g /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/output_log_path.log -nt 0\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log2.err:cmd_wrapper.py:60                 :-) GROMACS - gmx mdrun, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/grompp_mdrun\nCommand line:\n  gmx -nobackup -nocopyright mdrun -o /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/output_trr_path.trr -s /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/internal.tpr -c /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/output_gro_path.gro -e /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/output_edr_path.edr -g /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/output_log_path.log -nt 0\n\nReading file /tmp/biobb/unitests_107/grompp_mdrun/6eb16e4a-6482-4be1-9b00-a21b9cea823a/internal.tpr, VERSION 2022.2-conda_forge (single precision)\nChanging nstlist from 10 to 100, rlist from 1 to 1\n\nUsing 1 MPI thread\nUsing 4 OpenMP threads \n\nstarting mdrun &amp;#x27;Protein in water&amp;#x27;\n5000 steps,      0.5 ps.\n\nWriting final coordinates.\n\n               Core t (s)   Wall t (s)        (%)\n       Time:      258.639       64.660      400.0\n                 (ns/day)    (hour/ns)\nPerformance:        0.668       35.915\n\nGROMACS reminds you: &amp;quot;Right Now My Job is Eating These Doughnuts&amp;quot; (Bodycount)\n\n\nINFO     /tmp/biobb/unitests_107/grompp_mdrun/grompp_mdrun_log.out:file_utils.py:391 MDRun return code: 0\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py::TestMakeNdx::test_make_ndx&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py::TestMakeNdx::test_make_ndx&#34;, &#34;duration&#34;: &#34;110 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_make_ndx.py::TestMakeNdx::test_make_ndx&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;110 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/make_ndx/output_ndx.ndx\nComparing: \n        File_A: /tmp/biobb/unitests_107/make_ndx/output_ndx.ndx\n        File_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_make_ndx_protein_dna.ndx\n        File_A hash: b&amp;#x27;\\xd7i\\x10P\\xf5\\x975\\xfe&amp;lt;X\\xaaf\\x83H\\x14i\\x0f\\xd1=I\\xa3\\xb92?\\xaa\\xf7\\x10\\xf0U\\xdb\\x90\\xa9&amp;#x27;\n        File_B hash: b&amp;#x27;\\xd7i\\x10P\\xf5\\x975\\xfe&amp;lt;X\\xaaf\\x83H\\x14i\\x0f\\xd1=I\\xa3\\xb92?\\xaa\\xf7\\x10\\xf0U\\xdb\\x90\\xa9&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     30300938-f85c-4315-8b36-05798297b3bb/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     30300938-f85c-4315-8b36-05798297b3bb/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     30300938-f85c-4315-8b36-05798297b3bb/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/make_ndx\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.make_ndx Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/make_ndx_protein_dna.pdb to /tmp/biobb/unitests_107/make_ndx/b41b0f99-e4d5-4f08-8fd8-7d143d7b7ff3\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/make_ndx/52e2efe7-8f7f-42a2-a3fd-a86db4c21ff2.stdin to /tmp/biobb/unitests_107/make_ndx/b41b0f99-e4d5-4f08-8fd8-7d143d7b7ff3\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright make_ndx -f /tmp/biobb/unitests_107/make_ndx/b41b0f99-e4d5-4f08-8fd8-7d143d7b7ff3/make_ndx_protein_dna.pdb -o /tmp/biobb/unitests_107/make_ndx/b41b0f99-e4d5-4f08-8fd8-7d143d7b7ff3/output_ndx.ndx &amp;lt; /tmp/biobb/unitests_107/make_ndx/b41b0f99-e4d5-4f08-8fd8-7d143d7b7ff3/52e2efe7-8f7f-42a2-a3fd-a86db4c21ff2.stdin\n\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.out:cmd_wrapper.py:52 Going to read 0 old index file(s)\nAnalysing residue names:\nThere are:   292    Protein residues\nThere are:    46        DNA residues\nAnalysing Protein...\n\n  0 System              :  3063 atoms\n  1 Protein             :  2126 atoms\n  2 Protein-H           :  2126 atoms\n  3 C-alpha             :   292 atoms\n  4 Backbone            :   876 atoms\n  5 MainChain           :  1168 atoms\n  6 MainChain+Cb        :  1448 atoms\n  7 MainChain+H         :  1168 atoms\n  8 SideChain           :   958 atoms\n  9 SideChain-H         :   958 atoms\n 10 Prot-Masses         :  2126 atoms\n 11 non-Protein         :   937 atoms\n 12 DNA                 :   937 atoms\n\n nr : group      &amp;#x27;!&amp;#x27;: not  &amp;#x27;name&amp;#x27; nr name   &amp;#x27;splitch&amp;#x27; nr    Enter: list groups\n &amp;#x27;a&amp;#x27;: atom       &amp;#x27;&amp;amp;&amp;#x27;: and  &amp;#x27;del&amp;#x27; nr         &amp;#x27;splitres&amp;#x27; nr   &amp;#x27;l&amp;#x27;: list residues\n &amp;#x27;t&amp;#x27;: atom type  &amp;#x27;|&amp;#x27;: or   &amp;#x27;keep&amp;#x27; nr        &amp;#x27;splitat&amp;#x27; nr    &amp;#x27;h&amp;#x27;: help\n &amp;#x27;r&amp;#x27;: residue              &amp;#x27;res&amp;#x27; nr         &amp;#x27;chain&amp;#x27; char\n &amp;quot;name&amp;quot;: group             &amp;#x27;case&amp;#x27;: case sensitive           &amp;#x27;q&amp;#x27;: save and quit\n &amp;#x27;ri&amp;#x27;: residue index\n\n&amp;gt; \nFound 1808 atoms with name C*\n\n 13 C*                  :  1808 atoms\n\n&amp;gt; \nCopied index group 0 &amp;#x27;System&amp;#x27;\nCopied index group 13 &amp;#x27;C*&amp;#x27;\nComplemented group: 1255 atoms\nMerged two groups with AND: 3063 1255 -&amp;gt; 1255\n\n 14 System_&amp;amp;_!C*        :  1255 atoms\n\n&amp;gt; \n\n&amp;gt; \n\nINFO     /tmp/biobb/unitests_107/make_ndx/make_ndx_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx make_ndx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/make_ndx\nCommand line:\n  gmx -nobackup -nocopyright make_ndx -f /tmp/biobb/unitests_107/make_ndx/b41b0f99-e4d5-4f08-8fd8-7d143d7b7ff3/make_ndx_protein_dna.pdb -o /tmp/biobb/unitests_107/make_ndx/b41b0f99-e4d5-4f08-8fd8-7d143d7b7ff3/output_ndx.ndx\n\n\nReading structure file\n\nGROMACS reminds you: &amp;quot;Right Now My Job is Eating These Doughnuts&amp;quot; (Bodycount)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py::TestMdrun::test_mdrun&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py::TestMdrun::test_mdrun&#34;, &#34;duration&#34;: &#34;00:01:50&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_mdrun.py::TestMdrun::test_mdrun&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:50&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/mdrun/output_trr_path.trr\nComparing GROMACS files:\nFILE_A: /tmp/biobb/unitests_107/mdrun/output_trr_path.trr\nFILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_mdrun.trr\n\ncmd_wrapper commnand print: echo &amp;quot;Protein Protein&amp;quot; | gmx rms -s /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/mdrun.tpr -f /tmp/biobb/unitests_107/mdrun/output_trr_path.trr -f2 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_mdrun.trr -xvg none\nExit, code 0\nResult file: /tmp/biobb/unitests_107/mdrun/rmsd.xvg\nChecking if empty file: /tmp/biobb/unitests_107/mdrun/output_gro_path.gro\nChecking if empty file: /tmp/biobb/unitests_107/mdrun/output_edr_path.edr\nChecking if empty file: /tmp/biobb/unitests_107/mdrun/output_log_path.log\n\n------------------------------ Captured log call -------------------------------\nINFO     3289e437-ae28-4a2a-929c-9bc81db86ae6/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     3289e437-ae28-4a2a-929c-9bc81db86ae6/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     3289e437-ae28-4a2a-929c-9bc81db86ae6/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/mdrun\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.mdrun Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/mdrun.tpr to /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:file_utils.py:391 User added number of gmx threads: 0\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright mdrun -o /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/output_trr_path.trr -s /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/mdrun.tpr -c /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/output_gro_path.gro -e /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/output_edr_path.edr -g /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/output_log_path.log -nt 0\n\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/mdrun/mdrun_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx mdrun, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/mdrun\nCommand line:\n  gmx -nobackup -nocopyright mdrun -o /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/output_trr_path.trr -s /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/mdrun.tpr -c /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/output_gro_path.gro -e /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/output_edr_path.edr -g /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/output_log_path.log -nt 0\n\nReading file /tmp/biobb/unitests_107/mdrun/86792e7a-69fe-4c75-ad30-20755b2b7b8d/mdrun.tpr, VERSION 2018.1 (single precision)\nNote: file tpx version 112, software tpx version 127\nChanging nstlist from 10 to 40, rlist from 1 to 1.096\n\nUsing 1 MPI thread\nUsing 4 OpenMP threads \n\nstarting mdrun &amp;#x27;Protein in water&amp;#x27;\n15000 steps,     30.0 ps.\n\nWriting final coordinates.\n\n               Core t (s)   Wall t (s)        (%)\n       Time:      431.409      107.852      400.0\n                 (ns/day)    (hour/ns)\nPerformance:       24.034        0.999\n\nGROMACS reminds you: &amp;quot;They don&amp;#x27;t have any beavers in India, so they have to simulate them&amp;quot; (The Tubes)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py::TestPdb2gmx::test_pdb2gmx&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py::TestPdb2gmx::test_pdb2gmx&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_pdb2gmx.py::TestPdb2gmx::test_pdb2gmx&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/pdb2gmx/output_top_zip.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_107/pdb2gmx/output_top_zip.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_pdb2gmx.zip\nComparing TOP/ITP:\n     FILE_A: 043a6049-a9d2-4fb0-a86c-627467bb2b4c/pdb2gmx_p2g.top\n     FILE_B: de3370de-06b6-4cd3-b46e-2c45fb40d900/pdb2gmx_p2g.top\nComparing TOP/ITP:\n     FILE_A: 043a6049-a9d2-4fb0-a86c-627467bb2b4c/pdb2gmx_posre.itp\n     FILE_B: de3370de-06b6-4cd3-b46e-2c45fb40d900/pdb2gmx_posre.itp\nChecking if empty file: /tmp/biobb/unitests_107/pdb2gmx/output_gro.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_107/pdb2gmx/output_gro.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_pdb2gmx.gro\n\n------------------------------ Captured log call -------------------------------\nINFO     4b7d1c7f-b3d2-45c1-b880-8d85213428a2/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     4b7d1c7f-b3d2-45c1-b880-8d85213428a2/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     4b7d1c7f-b3d2-45c1-b880-8d85213428a2/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/pdb2gmx\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.pdb2gmx Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/egfr.pdb to /tmp/biobb/unitests_107/pdb2gmx/c6fed4a9-4805-4af0-b73c-4fd0f320ad08\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Copy: /tmp/biobb/unitests_107/pdb2gmx/1b84f83a-815e-469a-91ac-c7dd6ae3d224.stdin to /tmp/biobb/unitests_107/pdb2gmx/c6fed4a9-4805-4af0-b73c-4fd0f320ad08\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright pdb2gmx -f /tmp/biobb/unitests_107/pdb2gmx/c6fed4a9-4805-4af0-b73c-4fd0f320ad08/egfr.pdb -o /tmp/biobb/unitests_107/pdb2gmx/c6fed4a9-4805-4af0-b73c-4fd0f320ad08/output_gro.gro -p pdb2gmx_p2g.top -water spce -ff amber99sb-ildn -i pdb2gmx_posre.itp -his &amp;lt; /tmp/biobb/unitests_107/pdb2gmx/c6fed4a9-4805-4af0-b73c-4fd0f320ad08/1b84f83a-815e-469a-91ac-c7dd6ae3d224.stdin\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:cmd_wrapper.py:52 Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff\n\ngoing to rename amber99sb-ildn.ff/aminoacids.r2b\n\ngoing to rename amber99sb-ildn.ff/dna.r2b\n\ngoing to rename amber99sb-ildn.ff/rna.r2b\nReading /tmp/biobb/unitests_107/pdb2gmx/c6fed4a9-4805-4af0-b73c-4fd0f320ad08/egfr.pdb...\nRead &amp;#x27;Protein in water&amp;#x27;, 4698 atoms\n\nAnalyzing pdb file\nSplitting chemical chains based on TER records or chain id changing.\n\nThere are 1 chains and 0 blocks of water and 291 residues with 4698 atoms\n\n  chain  #res #atoms\n\n  1 &amp;#x27; &amp;#x27;   291   4698  \n\nAll occupancies are one\n\nReading residue database... (Amber99sb-ildn)\n\nProcessing chain 1 (4698 atoms, 291 residues)\nWhich HISTIDINE type do you want for residue 80\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 112\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 142\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 157\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 177\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 195\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:Which HISTIDINE type do you want for residue 200\n0. H on ND1 only (HID)\n1. H on NE2 only (HIE)\n2. H on ND1 and NE2 (HIP)\n3. Coupled to Heme (HIS1)\n\nType a number:\nIdentified residue ALA694 as a starting terminus.\n\nIdentified residue ASP984 as a ending terminus.\n\nChecking for duplicate atoms....\n\nGenerating any missing hydrogen atoms and/or adding termini.\n\nNow there are 291 residues with 4698 atoms\n\nMaking bonds...\n\nNumber of bonds was 4750, now 4749\n\nGenerating angles, dihedrals and pairs...\n\nMaking cmap torsions...\n\nThere are 13015 dihedrals,  885 impropers, 8643 angles\n          12439 pairs,     4749 bonds and     0 virtual sites\n\nTotal mass 33034.844 a.m.u.\n\nTotal charge 1.000 e\n\nWriting topology\n\nWriting coordinate file...\n\n\t\t--------- PLEASE NOTE ------------\n\nYou have successfully generated a topology from: /tmp/biobb/unitests_107/pdb2gmx/c6fed4a9-4805-4af0-b73c-4fd0f320ad08/egfr.pdb.\n\nThe Amber99sb-ildn force field and the spce water model are used.\n\n\t\t--------- ETON ESAELP ------------\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx pdb2gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/pdb2gmx\nCommand line:\n  gmx -nobackup -nocopyright pdb2gmx -f /tmp/biobb/unitests_107/pdb2gmx/c6fed4a9-4805-4af0-b73c-4fd0f320ad08/egfr.pdb -o /tmp/biobb/unitests_107/pdb2gmx/c6fed4a9-4805-4af0-b73c-4fd0f320ad08/output_gro.gro -p pdb2gmx_p2g.top -water spce -ff amber99sb-ildn -i pdb2gmx_posre.itp -his\n\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/dna.r2b\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/rna.r2b\nAll occupancies are one\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/dna.rtp\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/rna.rtp\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/dna.hdb\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/rna.hdb\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb\n8 out of 8 lines of specbond.dat converted successfully\nSpecial Atom Distance matrix:\n                  MET695  MET766 HISD773  CYS775  CYS781  MET793  CYS797\n                    SD23  SD1165 NE21261  SG1289  SG1388  SD1581  SG1636\n  MET766  SD1165   2.050\n HISD773 NE21261   2.326   1.712\n  CYS775  SG1289   2.164   0.449   1.373\n  CYS781  SG1388   2.773   1.629   3.094   1.807\n  MET793  SD1581   2.494   0.945   1.126   0.509   2.146\n  CYS797  SG1636   3.260   1.426   1.690   1.216   2.628   0.992\n HISD805 NE21778   4.161   2.554   2.115   2.186   3.416   1.721   1.389\n  CYS818  SG1989   3.418   2.358   1.312   2.084   3.856   1.769   1.505\n  MET825  SD2094   2.430   1.467   1.209   1.395   3.095   1.413   1.411\n HISE835 NE22276   2.416   1.048   1.540   1.110   2.637   1.276   1.201\n HISE850 NE22524   2.350   1.478   0.515   1.070   2.695   0.750   1.522\n HISD870 NE22846   3.369   2.871   3.404   3.131   4.127   3.395   3.126\n  MET881  SD3017   3.150   2.072   2.344   2.185   3.555   2.299   1.872\n HISD888 NE23129   4.108   3.391   3.630   3.562   4.763   3.706   3.230\n HISD893 NE23224   2.060   1.912   1.753   1.983   3.456   2.151   2.308\n  MET908  SD3462   3.928   2.747   1.769   2.463   4.179   2.107   1.670\n  CYS939  SG3932   4.321   3.174   2.232   2.925   4.631   2.597   2.071\n  MET945  SD4028   4.384   3.693   2.561   3.489   5.271   3.236   2.889\n  MET947  SD4064   4.014   2.907   2.096   2.711   4.426   2.454   1.925\n  CYS950  SG4116   3.368   2.551   1.832   2.435   4.163   2.310   1.989\n  MET952  SD4154   4.094   3.464   2.854   3.419   5.066   3.345   2.931\n  MET971  SD4479   3.836   3.087   1.768   2.809   4.605   2.492   2.299\n                 HISD805  CYS818  MET825 HISE835 HISE850 HISD870  MET881\n                 NE21778  SG1989  SD2094 NE22276 NE22524 NE22846  SD3017\n  CYS818  SG1989   1.803\n  MET825  SD2094   2.465   1.251\n HISE835 NE22276   2.481   1.663   0.593\n HISE850 NE22524   1.892   1.588   1.448   1.597\n HISD870 NE22846   4.415   3.189   2.239   2.125   3.622\n  MET881  SD3017   3.085   1.917   1.143   1.081   2.541   1.354\n HISD888 NE23129   4.366   3.052   2.455   2.462   3.898   0.983   1.409\n HISD893 NE23224   3.384   1.999   0.933   1.207   2.071   1.824   1.336\n  MET908  SD3462   1.686   0.517   1.711   2.057   1.984   3.488   2.189\n  CYS939  SG3932   2.082   0.934   2.031   2.388   2.486   3.534   2.294\n  MET945  SD4028   3.071   1.494   2.302   2.796   2.967   3.461   2.492\n  MET947  SD4064   2.260   0.820   1.664   2.028   2.384   3.044   1.827\n  CYS950  SG4116   2.700   0.996   1.115   1.577   2.204   2.388   1.296\n  MET952  SD4154   3.632   1.971   2.049   2.430   3.254   2.308   1.694\n  MET971  SD4479   2.353   0.799   1.845   2.352   2.146   3.564   2.417\n                 HISD888 HISD893  MET908  CYS939  MET945  MET947  CYS950\n                 NE23129 NE23224  SD3462  SG3932  SD4028  SD4064  SG4116\n HISD893 NE23224   2.240\n  MET908  SD3462   3.227   2.469\n  CYS939  SG3932   3.131   2.697   0.518\n  MET945  SD4028   2.985   2.620   1.396   1.079\n  MET947  SD4064   2.661   2.276   0.667   0.493   1.032\n  CYS950  SG4116   2.161   1.486   1.260   1.299   1.268   0.843\n  MET952  SD4154   1.734   2.061   2.064   1.840   1.308   1.439   1.062\n  MET971  SD4479   3.301   2.354   0.817   0.874   0.907   0.926   1.181\n                  MET952\n                  SD4154\n  MET971  SD4479   1.846\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/dna.arn\nOpening force field file /home/user/micromamba/envs/test_environment/share/gromacs/top/amber99sb-ildn.ff/rna.arn\nBefore cleaning: 12511 pairs\nBefore cleaning: 13015 dihedrals\n\nGROMACS reminds you: &amp;quot;If you thought that science was certain - well, that is just an error on your part.&amp;quot; (Richard Feynman)\n\n\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_107/pdb2gmx/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:203 Ignored file amber99sb-ildn.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:203 Ignored file amber99sb-ildn.ff/spce.itp\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:203 Ignored file amber99sb-ildn.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:149 [&amp;#x27;pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;pdb2gmx_posre.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:150 to: /tmp/biobb/unitests_107/pdb2gmx/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/pdb2gmx/pdb2gmx_log.out:file_utils.py:391 Removed: [&amp;#x27;pdb2gmx_posre.itp&amp;#x27;, &amp;#x27;pdb2gmx_p2g.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_solvate.py::TestSolvate::test_solvate&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_solvate.py::TestSolvate::test_solvate&#34;, &#34;duration&#34;: &#34;743 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_solvate.py::TestSolvate::test_solvate&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;743 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/solvate/output_gro.gro\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_107/solvate/output_gro.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_solvate.gro\nChecking if empty file: /tmp/biobb/unitests_107/solvate/output_top_zip.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_107/solvate/output_top_zip.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_solvate.zip\nComparing TOP/ITP:\n     FILE_A: c55d47cf-06b3-4881-8cb9-079b0f4a3092/A.Lys58Glu_step4_p2g_p2g.itp\n     FILE_B: d34684f4-4cb0-41e6-bf96-6da716ababc2/A.Lys58Glu_step4_p2g_p2g.itp\nComparing TOP/ITP:\n     FILE_A: c55d47cf-06b3-4881-8cb9-079b0f4a3092/A.Lys58Glu_step4_p2g_p2g.top\n     FILE_B: d34684f4-4cb0-41e6-bf96-6da716ababc2/A.Lys58Glu_step4_p2g_p2g.top\n\n------------------------------ Captured log call -------------------------------\nINFO     6b907678-970f-4c59-b310-dd62f7f8ac9a/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     6b907678-970f-4c59-b310-dd62f7f8ac9a/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     6b907678-970f-4c59-b310-dd62f7f8ac9a/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/solvate\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.solvate Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/solvate.gro to /tmp/biobb/unitests_107/solvate/678e6991-a2bd-4484-bb57-cbf0e7f18212\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/solvate.zip\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:174 [&amp;#x27;780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/solvate.zip\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:256 780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.itp\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:256 780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.top\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright solvate -cp /tmp/biobb/unitests_107/solvate/678e6991-a2bd-4484-bb57-cbf0e7f18212/solvate.gro -cs spc216.gro -o /tmp/biobb/unitests_107/solvate/678e6991-a2bd-4484-bb57-cbf0e7f18212/output_gro.gro -p 780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.top\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:cmd_wrapper.py:52 \nWARNING: Masses and atomic (Van der Waals) radii will be guessed\n         based on residue and atom names, since they could not be\n         definitively assigned from the information in your input\n         files. These guessed numbers might deviate from the mass\n         and radius of the atom type. Please check the output\n         files if necessary. Note, that this functionality may\n         be removed in a future GROMACS version. Please, consider\n         using another file format for your input.\n\nNOTE: From version 5.0 gmx solvate uses the Van der Waals radii\nfrom the source below. This means the results may be different\ncompared to previous GROMACS versions.\n\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\nA. Bondi\nvan der Waals Volumes and Radii\nJ. Phys. Chem. 68 (1964) pp. 441-451\n-------- -------- --- Thank You --- -------- --------\n\nAdding line for 23502 solvent molecules with resname (SOL) to topology file (780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.top)\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.err:cmd_wrapper.py:60                :-) GROMACS - gmx solvate, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/solvate\nCommand line:\n  gmx -nobackup -nocopyright solvate -cp /tmp/biobb/unitests_107/solvate/678e6991-a2bd-4484-bb57-cbf0e7f18212/solvate.gro -cs spc216.gro -o /tmp/biobb/unitests_107/solvate/678e6991-a2bd-4484-bb57-cbf0e7f18212/output_gro.gro -p 780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.top\n\nReading solute configuration\nReading solvent configuration\n\nInitialising inter-atomic distances...\nGenerating solvent configuration\nWill generate new solvent configuration of 5x5x5 boxes\nSolvent box contains 80550 atoms in 26850 residues\nRemoved 8835 solvent atoms due to solvent-solvent overlap\nRemoved 1209 solvent atoms due to solute-solvent overlap\nSorting configuration\nFound 1 molecule type:\n    SOL (   3 atoms): 23502 residues\nGenerated solvent containing 70506 atoms in 23502 residues\nWriting generated configuration to /tmp/biobb/unitests_107/solvate/678e6991-a2bd-4484-bb57-cbf0e7f18212/output_gro.gro\n\nOutput configuration contains 71702 atoms in 23581 residues\nVolume                 :      729.19 (nm^3)\nDensity                :     985.432 (g/l)\nNumber of solvent molecules:  23502   \n\nProcessing topology\n\nGROMACS reminds you: &amp;quot;Cowardly refusing to create an empty archive&amp;quot; (GNU tar)\n\n\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_107/solvate/678e6991-a2bd-4484-bb57-cbf0e7f18212/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:203 Ignored file 780b8ba0-130f-4680-89af-721c77124821/amber99sb-ildn.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:203 Ignored file 780b8ba0-130f-4680-89af-721c77124821/amber99sb-ildn.ff/spce.itp\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:203 Ignored file 780b8ba0-130f-4680-89af-721c77124821/amber99sb-ildn.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:149 [&amp;#x27;780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:150 to: /tmp/biobb/unitests_107/solvate/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/solvate/solvate_log.out:file_utils.py:391 Removed: [&amp;#x27;780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.itp&amp;#x27;, &amp;#x27;780b8ba0-130f-4680-89af-721c77124821/A.Lys58Glu_step4_p2g_p2g.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py::TestSolvate::test_solvate&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py::TestSolvate::test_solvate&#34;, &#34;duration&#34;: &#34;260 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs/test_trjcat.py::TestSolvate::test_solvate&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;260 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/trjcat/output_trjcat.trr\nComparing: \n        File_A: /tmp/biobb/unitests_107/trjcat/output_trjcat.trr\n        File_B: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs/ref_trjcat.trr\n        File_A hash: b&amp;#x27;\\x0f\\xc2\\xe1L\\xf6V&amp;amp;\\x05\\x8e\\xae\\xb5\\xdf\\x9aJD1d\\xf5\\x1bl\\x9b\\xda\\x82Fd\\x96\\xf1)&amp;amp;\\x0f6\\xef&amp;#x27;\n        File_B hash: b&amp;#x27;\\x0f\\xc2\\xe1L\\xf6V&amp;amp;\\x05\\x8e\\xae\\xb5\\xdf\\x9aJD1d\\xf5\\x1bl\\x9b\\xda\\x82Fd\\x96\\xf1)&amp;amp;\\x0f6\\xef&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     b9679034-8046-4e9d-aa19-2875b0969b0c/log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright -version\n\nINFO     b9679034-8046-4e9d-aa19-2875b0969b0c/log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     b9679034-8046-4e9d-aa19-2875b0969b0c/log.out:cmd_wrapper.py:52                    :-) GROMACS - gmx, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/trjcat\nCommand line:\n  gmx -nobackup -nocopyright -version\n\nGROMACS version:    2022.2-conda_forge\nPrecision:          mixed\nMemory model:       64 bit\nMPI library:        thread_mpi\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)\nGPU support:        OpenCL\nSIMD instructions:  AVX2_256\nCPU FFT library:    fftw-3.3.10-sse2-avx\nGPU FFT library:    clFFT\nRDTSCP usage:       enabled\nTNG support:        enabled\nHwloc support:      disabled\nTracing support:    disabled\nC compiler:         /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 10.3.0\nC compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG\nC++ compiler:       /home/conda/feedstock_root/build_artifacts/gromacs_1657275263449/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 10.3.0\nC++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG\nOpenCL include dir: /home/user/micromamba/envs/test_environment/include\nOpenCL library:     /home/user/micromamba/envs/test_environment/lib/libOpenCL.so\nOpenCL version:     2.2\n\n\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs.trjcat Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs/trjcat.zip\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:174 [&amp;#x27;625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_a.trr&amp;#x27;, &amp;#x27;625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_b.trr&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:file_utils.py:391 Only concatenate the files without removal of frames with identical timestamps.\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:cmd_wrapper.py:33 gmx -nobackup -nocopyright trjcat -f 625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_a.trr 625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_b.trr -o /tmp/biobb/unitests_107/trjcat/2d893a09-9961-427f-bd47-e283a04d76e2/output_trjcat.trr -cat\n\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.out:cmd_wrapper.py:52 Note that major changes are planned in future for trjcat, to improve usability and utility.\nlasttime 0\n\nlasttime 30\n\nINFO     /tmp/biobb/unitests_107/trjcat/trjcat_log.err:cmd_wrapper.py:60                 :-) GROMACS - gmx trjcat, 2022.2-conda_forge (-:\n\nExecutable:   /home/user/micromamba/envs/test_environment/bin.AVX2_256/gmx\nData prefix:  /home/user/micromamba/envs/test_environment\nWorking dir:  /tmp/biobb/unitests_107/trjcat\nCommand line:\n  gmx -nobackup -nocopyright trjcat -f 625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_a.trr 625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_b.trr -o /tmp/biobb/unitests_107/trjcat/2d893a09-9961-427f-bd47-e283a04d76e2/output_trjcat.trr -cat\n\ntrr version: GMX_trn_file (single precision)\n\rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \rReading frame       0 time    0.000   \rReading frame       1 time   10.000   \n\nSummary of files and start times used:\n\n          File                Start time       Time step\n---------------------------------------------------------\n625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_a.trr        0.000 ps       10.000 ps\n625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_b.trr        0.000 ps       10.000 ps WARNING: same Start time as previous\n\n\rReading frame       0 time    0.000   \nContinue writing frames from 625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_a.trr t=0 ps, frame=0      \n -&amp;gt;  frame      0 time    0.000 ps     \r\rReading frame       1 time   10.000    -&amp;gt;  frame      1 time   10.000 ps     \r\rReading frame       2 time   20.000    -&amp;gt;  frame      2 time   20.000 ps     \r\rReading frame       3 time   30.000    -&amp;gt;  frame      3 time   30.000 ps     \r\rLast frame          3 time   30.000   \n\rReading frame       0 time    0.000   \nContinue writing frames from 625fe789-e7c5-4966-b01d-b7e20581b6e1/ref_trjcat_b.trr t=0 ps, frame=4      \n -&amp;gt;  frame      4 time    0.000 ps     \r\rReading frame       1 time   10.000    -&amp;gt;  frame      5 time   10.000 ps     \r\rReading frame       2 time   20.000    -&amp;gt;  frame      6 time   20.000 ps     \r\rReading frame       3 time   30.000    -&amp;gt;  frame      7 time   30.000 ps     \r\rLast frame          3 time   30.000   \n\nLast frame written was 7, time 30.000000 ps\n\nGROMACS reminds you: &amp;quot;A cop pulls Heisenberg over and asks him &amp;#x27;Do you know how fast you were going?&amp;#x27; Heisenberg replies &amp;#x27;No, but I know exactly where I am&amp;#x27;. The cop says &amp;#x27;You were doing 55 in a 35 zone&amp;#x27;. Heisenberg: &amp;#x27;Great! Now I&amp;#x27;m lost!&amp;quot; (Anonymous)\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py::TestAppendLigand::test_append_ligand&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py::TestAppendLigand::test_append_ligand&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs_extra/test_append_ligand.py::TestAppendLigand::test_append_ligand&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/append_ligand/output_top_zip.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_107/append_ligand/output_top_zip.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs_extra/ref_appendligand.zip\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/append_ligand_ligand.top\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/append_ligand_ligand.top\nComparing TOP/ITP:\n     FILE_A: 6df72a86-eeec-4733-b06e-e9435de687f0/pep_ligand.itp\n     FILE_B: fe9eb298-fd6a-481e-9651-d09877945aea/pep_ligand.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs_extra.append_ligand Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:174 [&amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step8_gio_gio.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:256 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step8_gio_gio.top\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_107/append_ligand/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:203 Ignored file 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/amber99sb.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:203 Ignored file 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/posre_PEP-H.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:203 Ignored file 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/amber99sb.ff/tip3p.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:203 Ignored file 5fde2f66-5f2e-4c1b-8b5c-60a15487996f/amber99sb.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:149 [&amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/append_ligand_ligand.top&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/pep_ligand.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:150 to: /tmp/biobb/unitests_107/append_ligand/output_top_zip.zip\nINFO     /tmp/biobb/unitests_107/append_ligand/append_ligand_log.out:file_utils.py:391 Removed: [&amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/pep_ligand.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27;, &amp;#x27;5fde2f66-5f2e-4c1b-8b5c-60a15487996f/append_ligand_ligand.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py::TestNdx2resttop::test_ndx2resttop&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py::TestNdx2resttop::test_ndx2resttop&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_gromacs/test/unitests/test_gromacs_extra/test_ndx2resttop.py::TestNdx2resttop::test_ndx2resttop&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nChecking if empty file: /tmp/biobb/unitests_107/ndx2resttop/output_top_zip.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_107/ndx2resttop/output_top_zip.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/reference/gromacs_extra/ref_ndx2resttop.zip\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ALL.Ala115Pro_step8_gio_gio.top\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ALL.Ala115Pro_step8_gio_gio.top\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ndx2resttop_Chain_A_noMut.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ndx2resttop_Chain_A_noMut.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ndx2resttop_Chain_B_noMut.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ndx2resttop_Chain_B_noMut.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ndx2resttop_Chain_C_noMut.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ndx2resttop_Chain_C_noMut.itp\nComparing TOP/ITP:\n     FILE_A: 912736ff-856c-4832-89b2-fda874d0916e/ndx2resttop_Chain_D_noMut.itp\n     FILE_B: 616a89d9-7c73-4790-ba7f-d3f41303442c/ndx2resttop_Chain_D_noMut.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Executing biobb_gromacs.gromacs_extra.ndx2resttop Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:174 [&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step8_gio_gio.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_gromacs/biobb_gromacs/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:256 76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step8_gio_gio.top\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Index_dic: {&amp;#x27;[ System ]&amp;#x27;: (0,), &amp;#x27;[ Protein ]&amp;#x27;: (26363, 26363), &amp;#x27;[ Protein-H ]&amp;#x27;: (28474, 28474), &amp;#x27;[ C-alpha ]&amp;#x27;: (29520, 29520), &amp;#x27;[ Backbone ]&amp;#x27;: (29659, 29659), &amp;#x27;[ MainChain ]&amp;#x27;: (30074, 30074), &amp;#x27;[ MainChain+Cb ]&amp;#x27;: (30627, 30627), &amp;#x27;[ MainChain+H ]&amp;#x27;: (31306, 31306), &amp;#x27;[ SideChain ]&amp;#x27;: (31990, 31990), &amp;#x27;[ SideChain-H ]&amp;#x27;: (33418, 33418), &amp;#x27;[ Prot-Masses ]&amp;#x27;: (33912, 33912), &amp;#x27;[ non-Protein ]&amp;#x27;: (36023, 36023), &amp;#x27;[ Water ]&amp;#x27;: (60276, 60276), &amp;#x27;[ SOL ]&amp;#x27;: (84512, 84512), &amp;#x27;[ non-Water ]&amp;#x27;: (108748, 108748), &amp;#x27;[ Ion ]&amp;#x27;: (110876, 110876), &amp;#x27;[ NA ]&amp;#x27;: (110894, 110894), &amp;#x27;[ CL ]&amp;#x27;: (110904, 110904), &amp;#x27;[ Water_and_ions ]&amp;#x27;: (110914, 110914), &amp;#x27;[ Chain_A ]&amp;#x27;: (135167, 135167), &amp;#x27;[ Chain_B ]&amp;#x27;: (135696, 135696), &amp;#x27;[ Chain_C ]&amp;#x27;: (136225, 136225), &amp;#x27;[ Chain_D ]&amp;#x27;: (136754, 136754), &amp;#x27;[ Chain_A_noMut ]&amp;#x27;: (137283, 137283), &amp;#x27;[ Chain_B_noMut ]&amp;#x27;: (137545, 137545), &amp;#x27;[ Chain_C_noMut ]&amp;#x27;: (137807, 137807), &amp;#x27;[ Chain_D_noMut ]&amp;#x27;: (138069, 138069), &amp;#x27;[ Chain_A_backbone ]&amp;#x27;: (138331, 138331), &amp;#x27;[ Chain_B_backbone ]&amp;#x27;: (138470, 138470), &amp;#x27;[ Chain_C_backbone ]&amp;#x27;: (138609, 138609), &amp;#x27;[ Chain_D_backbone ]&amp;#x27;: (138748, 138748), &amp;#x27;[ Chain_all_noMut ]&amp;#x27;: (138887, 138887), &amp;#x27;[ Chain_all_backbone ]&amp;#x27;: (139932, 139932), &amp;#x27;[ Chain_A_Heavy ]&amp;#x27;: (140485, 140485), &amp;#x27;[ Chain_B_Heavy ]&amp;#x27;: (140748, 140748), &amp;#x27;[ Chain_C_Heavy ]&amp;#x27;: (141011, 141011), &amp;#x27;[ Chain_D_Heavy ]&amp;#x27;: (141274, 141536)}\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 ref_rest_chain_triplet_list: [(&amp;#x27;Chain_A&amp;#x27;, &amp;#x27;Chain_A_noMut&amp;#x27;, &amp;#x27;A&amp;#x27;), (&amp;#x27;Chain_B&amp;#x27;, &amp;#x27;Chain_B_noMut&amp;#x27;, &amp;#x27;B&amp;#x27;), (&amp;#x27;Chain_C&amp;#x27;, &amp;#x27;Chain_C_noMut&amp;#x27;, &amp;#x27;C&amp;#x27;), (&amp;#x27;Chain_D&amp;#x27;, &amp;#x27;Chain_D_noMut&amp;#x27;, &amp;#x27;D&amp;#x27;)]\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Reference group: Chain_A\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Restrain group: Chain_A_noMut\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Chain: A\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 reference_group_index: start_closed:135168 stop_open: 135167\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 restrain_group_index: start_closed:137284 stop_open: 137283\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Creating: &amp;lt;_io.TextIOWrapper name=&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ndx2resttop_Chain_A_noMut.itp&amp;#x27; mode=&amp;#x27;w&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the selected atoms force constants\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Opening: &amp;lt;_io.TextIOWrapper name=&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27; mode=&amp;#x27;a&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the ifdef include statement\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Reference group: Chain_B\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Restrain group: Chain_B_noMut\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Chain: B\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 reference_group_index: start_closed:135697 stop_open: 135696\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 restrain_group_index: start_closed:137546 stop_open: 137545\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Creating: &amp;lt;_io.TextIOWrapper name=&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ndx2resttop_Chain_B_noMut.itp&amp;#x27; mode=&amp;#x27;w&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the selected atoms force constants\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Opening: &amp;lt;_io.TextIOWrapper name=&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27; mode=&amp;#x27;a&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the ifdef include statement\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Reference group: Chain_C\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Restrain group: Chain_C_noMut\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Chain: C\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 reference_group_index: start_closed:136226 stop_open: 136225\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 restrain_group_index: start_closed:137808 stop_open: 137807\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Creating: &amp;lt;_io.TextIOWrapper name=&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ndx2resttop_Chain_C_noMut.itp&amp;#x27; mode=&amp;#x27;w&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the selected atoms force constants\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Opening: &amp;lt;_io.TextIOWrapper name=&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27; mode=&amp;#x27;a&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the ifdef include statement\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Reference group: Chain_D\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Restrain group: Chain_D_noMut\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Chain: D\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 reference_group_index: start_closed:136755 stop_open: 136754\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 restrain_group_index: start_closed:138070 stop_open: 138069\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Creating: &amp;lt;_io.TextIOWrapper name=&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ndx2resttop_Chain_D_noMut.itp&amp;#x27; mode=&amp;#x27;w&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the selected atoms force constants\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:391 Opening: &amp;lt;_io.TextIOWrapper name=&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27; mode=&amp;#x27;a&amp;#x27; encoding=&amp;#x27;UTF-8&amp;#x27;&amp;gt; and adding the ifdef include statement\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:203 Ignored file 76515800-cc5b-4d34-a719-50ff2c50d046/amber99sb.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:203 Ignored file 76515800-cc5b-4d34-a719-50ff2c50d046/amber99sb.ff/tip3p.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:203 Ignored file 76515800-cc5b-4d34-a719-50ff2c50d046/amber99sb.ff/ions.itp\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_107/ndx2resttop/ndx2resttop_log.out:file_utils.py:149 [&amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A_pr.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_B_pr.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_C_pr.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_D_pr.itp&amp;#x27;, &amp;#x27;76515800-cc5b-4d34-a719-50ff2c50d046/ALL.Ala115Pro_step8_gio_gio.top&amp;#x27;, 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