Skip to content

Commit

Permalink
Bug fixes
Browse files Browse the repository at this point in the history
  • Loading branch information
@gbayarri
gbayarri committed Jun 25, 2024
1 parent 65b7035 commit 5a06700
Show file tree
Hide file tree
Showing 3 changed files with 30 additions and 27 deletions.
19 changes: 10 additions & 9 deletions biobb_wf_md_setup/docs/source/tutorial.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,7 @@ if 'google.colab' in sys.modules:
```python
import nglview
import ipywidgets
import sys

pdbCode = "1AKI"
```
Expand Down Expand Up @@ -340,7 +341,7 @@ from biobb_gromacs.gromacs.grompp import grompp
# Create prop dict and inputs/outputs
output_gppion_tpr = pdbCode+'_gppion.tpr'
prop = {
'simulation_type': 'minimization',
'simulation_type': 'ions',
'maxwarn': 1
}

Expand Down Expand Up @@ -1074,16 +1075,16 @@ view
## Output files

Important **Output files** generated:
- {{output_md_gro}}: **Final structure** (snapshot) of the MD setup protocol.
- {{output_md_trr}}: **Final trajectory** of the MD setup protocol.
- {{output_md_cpt}}: **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.
- {{output_gppmd_tpr}}: **Final tpr file**, GROMACS portable binary run input file. This file contains the starting structure of the **MD setup free MD simulation step**, together with the molecular topology and all the simulation parameters. It can be used to **extend** the simulation.
- {{output_genion_top_zip}}: **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliary **include topology** files (.itp).
- **output_md_gro** (1aki_md.gro): **Final structure** (snapshot) of the MD setup protocol.
- **output_md_trr** (1aki_md.trr): **Final trajectory** of the MD setup protocol.
- **output_md_cpt** (1aki_md.cpt): **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.
- **output_gppmd_tpr** (1aki_gppmd.tpr): **Final tpr file**, GROMACS portable binary run input file. This file contains the starting structure of the **MD setup free MD simulation step**, together with the molecular topology and all the simulation parameters. It can be used to **extend** the simulation.
- **output_genion_top_zip** (1aki_genion_top.zip): **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliary **include topology** files (.itp).

**Analysis** (MD setup check) output files generated:
- {{output_rms_first}}: **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.
- {{output_rms_exp}}: **Root Mean Square deviation (RMSd)** against **experimental structure** of the final **free MD run step**.
- {{output_rgyr}}: **Radius of Gyration** of the final **free MD run step** of the **setup pipeline**.
- **output_rms_first** (1aki_rms_first.xvg): **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.
- **output_rms_exp** (1aki_rms_exp.xvg): **Root Mean Square deviation (RMSd)** against **experimental structure** of the final **free MD run step**.
- **output_rgyr** (1aki_rgyr.xvg): **Radius of Gyration** of the final **free MD run step** of the **setup pipeline**.


***
Expand Down
19 changes: 10 additions & 9 deletions biobb_wf_md_setup/html/biobb_wf_md_setup.web.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7656,6 +7656,7 @@ <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-pa
<div class="cm-editor cm-s-jupyter">
<div class="highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">nglview</span>
<span class="kn">import</span> <span class="nn">ipywidgets</span>
<span class="kn">import</span> <span class="nn">sys</span>

<span class="n">pdbCode</span> <span class="o">=</span> <span class="s2">"1AKI"</span>
</pre></div>
Expand Down Expand Up @@ -8120,7 +8121,7 @@ <h3 id="Step-1:-Creating-portable-binary-run-file-for-ion-generation">Step 1: Cr
<span class="c1"># Create prop dict and inputs/outputs</span>
<span class="n">output_gppion_tpr</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_gppion.tpr'</span>
<span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
<span class="s1">'simulation_type'</span><span class="p">:</span> <span class="s1">'minimization'</span><span class="p">,</span>
<span class="s1">'simulation_type'</span><span class="p">:</span> <span class="s1">'ions'</span><span class="p">,</span>
<span class="s1">'maxwarn'</span><span class="p">:</span> <span class="mi">1</span>
<span class="p">}</span>

Expand Down Expand Up @@ -9335,17 +9336,17 @@ <h3 id="Step-3:-Visualizing-the-generated-dehydrated-trajectory.">Step 3: Visual
<p><a id="output"></a></p>
<h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files"></a></h2><p>Important <strong>Output files</strong> generated:</p>
<ul>
<li>1AKI_md.gro: <strong>Final structure</strong> (snapshot) of the MD setup protocol.</li>
<li>1AKI_md.trr: <strong>Final trajectory</strong> of the MD setup protocol.</li>
<li>1AKI_md.cpt: <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
<li>1AKI_gppmd.tpr: <strong>Final tpr file</strong>, GROMACS portable binary run input file. This file contains the starting structure of the <strong>MD setup free MD simulation step</strong>, together with the molecular topology and all the simulation parameters. It can be used to <strong>extend</strong> the simulation.</li>
<li>1AKI_genion_top.zip: <strong>Final topology</strong> of the MD system. It is a compressed zip file including a <strong>topology file</strong> (.top) and a set of auxiliary <strong>include topology</strong> files (.itp).</li>
<li><strong>output_md_gro</strong> (1AKI_md.gro): <strong>Final structure</strong> (snapshot) of the MD setup protocol.</li>
<li><strong>output_md_trr</strong> (1AKI_md.trr): <strong>Final trajectory</strong> of the MD setup protocol.</li>
<li><strong>output_md_cpt</strong> (1AKI_md.cpt): <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
<li><strong>output_gppmd_tpr</strong> (1AKI_gppmd.tpr): <strong>Final tpr file</strong>, GROMACS portable binary run input file. This file contains the starting structure of the <strong>MD setup free MD simulation step</strong>, together with the molecular topology and all the simulation parameters. It can be used to <strong>extend</strong> the simulation.</li>
<li><strong>output_genion_top_zip</strong> (1AKI_genion_top.zip): <strong>Final topology</strong> of the MD system. It is a compressed zip file including a <strong>topology file</strong> (.top) and a set of auxiliary <strong>include topology</strong> files (.itp).</li>
</ul>
<p><strong>Analysis</strong> (MD setup check) output files generated:</p>
<ul>
<li>1AKI_rms_first.xvg: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
<li>1AKI_rms_exp.xvg: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
<li>1AKI_rgyr.xvg: <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
<li><strong>output_rms_first</strong> (1AKI_rms_first.xvg): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
<li><strong>output_rms_exp</strong> (1AKI_rms_exp.xvg): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
<li><strong>output_rgyr</strong> (1AKI_rgyr.xvg): <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
</ul>
</div>
</div>
Expand Down
19 changes: 10 additions & 9 deletions biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,7 @@
"source": [
"import nglview\n",
"import ipywidgets\n",
"import sys\n",
"\n",
"pdbCode = \"1AKI\""
]
Expand Down Expand Up @@ -465,7 +466,7 @@
"# Create prop dict and inputs/outputs\n",
"output_gppion_tpr = pdbCode+'_gppion.tpr'\n",
"prop = {\n",
" 'simulation_type': 'minimization',\n",
" 'simulation_type': 'ions',\n",
" 'maxwarn': 1\n",
"}\n",
"\n",
Expand Down Expand Up @@ -1408,16 +1409,16 @@
"## Output files\n",
"\n",
"Important **Output files** generated:\n",
" - {{output_md_gro}}: **Final structure** (snapshot) of the MD setup protocol.\n",
" - {{output_md_trr}}: **Final trajectory** of the MD setup protocol.\n",
" - {{output_md_cpt}}: **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.\n",
" - {{output_gppmd_tpr}}: **Final tpr file**, GROMACS portable binary run input file. This file contains the starting structure of the **MD setup free MD simulation step**, together with the molecular topology and all the simulation parameters. It can be used to **extend** the simulation.\n",
" - {{output_genion_top_zip}}: **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliary **include topology** files (.itp).\n",
" - **output_md_gro** (1aki_md.gro): **Final structure** (snapshot) of the MD setup protocol.\n",
" - **output_md_trr** (1aki_md.trr): **Final trajectory** of the MD setup protocol.\n",
" - **output_md_cpt** (1aki_md.cpt): **Final checkpoint file**, with information about the state of the simulation. It can be used to **restart** or **continue** a MD simulation.\n",
" - **output_gppmd_tpr** (1aki_gppmd.tpr): **Final tpr file**, GROMACS portable binary run input file. This file contains the starting structure of the **MD setup free MD simulation step**, together with the molecular topology and all the simulation parameters. It can be used to **extend** the simulation.\n",
" - **output_genion_top_zip** (1aki_genion_top.zip): **Final topology** of the MD system. It is a compressed zip file including a **topology file** (.top) and a set of auxiliary **include topology** files (.itp).\n",
"\n",
"**Analysis** (MD setup check) output files generated:\n",
" - {{output_rms_first}}: **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.\n",
" - {{output_rms_exp}}: **Root Mean Square deviation (RMSd)** against **experimental structure** of the final **free MD run step**.\n",
" - {{output_rgyr}}: **Radius of Gyration** of the final **free MD run step** of the **setup pipeline**.\n",
" - **output_rms_first** (1aki_rms_first.xvg): **Root Mean Square deviation (RMSd)** against **minimized and equilibrated structure** of the final **free MD run step**.\n",
" - **output_rms_exp** (1aki_rms_exp.xvg): **Root Mean Square deviation (RMSd)** against **experimental structure** of the final **free MD run step**.\n",
" - **output_rgyr** (1aki_rgyr.xvg): **Radius of Gyration** of the final **free MD run step** of the **setup pipeline**.\n",
" "
]
},
Expand Down

0 comments on commit 5a06700

Please sign in to comment.