From 4849099049fa643a145144bf950c917b4742a9e0 Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Mon, 17 Oct 2022 12:41:04 -0500 Subject: [PATCH 01/11] Add PTMA CG IBI model to polyply library [arXiv:2209.02072] --- polyply/data/ibi/PTMA.customexcl.ibi.ff | 65 +++++++++++++++++++++++++ polyply/data/ibi/citations.bib | 19 ++++++++ 2 files changed, 84 insertions(+) create mode 100644 polyply/data/ibi/PTMA.customexcl.ibi.ff create mode 100644 polyply/data/ibi/citations.bib diff --git a/polyply/data/ibi/PTMA.customexcl.ibi.ff b/polyply/data/ibi/PTMA.customexcl.ibi.ff new file mode 100644 index 00000000..3f55c420 --- /dev/null +++ b/polyply/data/ibi/PTMA.customexcl.ibi.ff @@ -0,0 +1,65 @@ +[ moleculetype ] +; name nexcl. +PTMA 2 + +[ atoms ] +; id type resnr residu atom cgnr charge mass + 1 VNL 1 PTMA VNL 1 0.0 54 + 2 EST 1 PTMA EST 2 0.0 54 + 3 C1 1 PTMA C1 3 0.0 54 + 4 C2 1 PTMA C2 4 0.0 54 + 5 C2 1 PTMA C3 5 0.0 54 + 6 N4 1 PTMA N4 6 0.0 36 + +[ bonds ] +; i j funct length + 1 2 1 0.262 15000 { "comment": "M3 PMMA model [10.1038/s41467-021-27627-4] shortened"} + 2 3 1 0.253 15000 { "comment": "PMMA-TEMPO connection"} + 3 4 1 0.326 25000 { "comment": "cog (TEMPO)"} + 3 5 1 0.326 25000 { "comment": "cog (TEMPO)"} + 3 6 1 0.310 100000 {"ifdef": "FLEXIBLE", "comment": "cog (TEMPO)"} + 4 6 1 0.238 100000 {"ifdef": "FLEXIBLE", "comment": "cog (TEMPO)"} + 5 6 1 0.238 100000 {"ifdef": "FLEXIBLE", "comment": "cog (TEMPO)"} + +[constraints] +; i j funct length + 3 6 1 0.310 {"ifndef": "FLEXIBLE", "comment": "cog (TEMPO)"} + 4 6 1 0.238 {"ifndef": "FLEXIBLE", "comment": "cog (TEMPO)"} + 5 6 1 0.238 {"ifndef": "FLEXIBLE", "comment": "cog (TEMPO)"} + +[ angles ] +; i j k funct length force k + 1 2 3 2 132.9 70 { "comment": "PMMA-TEMPO connection"} + 2 3 4 2 129.0 60 { "comment": "PMMA-TEMPO connection"} + 2 3 5 2 121.9 95 { "comment": "PMMA-TEMPO connection"} + +[dihedrals] +; i j k l funct ref.angle force_k + 3 4 5 6 2 140.00 20 { "comment": "cog (TEMPO)"} + 2 4 5 6 2 150.00 80 { "comment": "PMMA-TEMPO connection"} + +[exclusions] + 1 2 3 4 5 6 + 2 3 4 5 6 + 3 4 5 6 + 4 5 6 + 5 6 + +[ link ] +resname "PTMA" +[ bonds ] +VNL +VNL 1 0.315 4000 {"group": "vinyl backbone"} + +[ link ] +resname "PTMA" +[ angles ] +VNL +VNL ++VNL 2 115 35 {"group": "vinyl backbone"} + +[ link ] +resname "PTMA" +[ angles ] +EST VNL +VNL 2 70 20 + +[ citation ] +2022RAlessandri-arXiv +polyply diff --git a/polyply/data/ibi/citations.bib b/polyply/data/ibi/citations.bib new file mode 100644 index 00000000..bc8399e8 --- /dev/null +++ b/polyply/data/ibi/citations.bib @@ -0,0 +1,19 @@ +@article{2022RAlessandri-arXiv, + title={Predicting Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions}, + author={Alessandri, Riccardo and de Pablo, Juan J.}, + journal={arXiv}, + year={2022}, + eprint={2209.02072}, + primaryClass={cond-mat.soft}, + doi={https://doi.org/10.48550/arXiv.2209.02072} +} + +@article{polyply, + title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials}, + author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J}, + journal={Nature Communications}, + doi={10.1038/s41467-021-27627-4}, + year={2022}, + volume={13}, + pages={68} +} From 6730fba8e0ee180636cc2a5bee9d6cb0f9b21da6 Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Mon, 17 Oct 2022 13:00:15 -0500 Subject: [PATCH 02/11] Rename PTMA.customexcl.ibi.ff -> PTMA.CGM3.ibi.ff --- polyply/data/ibi/{PTMA.customexcl.ibi.ff => PTMA.CGM3.ibi.ff} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename polyply/data/ibi/{PTMA.customexcl.ibi.ff => PTMA.CGM3.ibi.ff} (100%) diff --git a/polyply/data/ibi/PTMA.customexcl.ibi.ff b/polyply/data/ibi/PTMA.CGM3.ibi.ff similarity index 100% rename from polyply/data/ibi/PTMA.customexcl.ibi.ff rename to polyply/data/ibi/PTMA.CGM3.ibi.ff From 1dad7ccf65779a03dc91362eec8d49c83b603d5c Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Mon, 21 Aug 2023 11:40:03 -0500 Subject: [PATCH 03/11] Update citation for PTMA.CGM3.ibi.ff --- polyply/data/ibi/PTMA.CGM3.ibi.ff | 2 +- polyply/data/ibi/citations.bib | 19 +++++++++++-------- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/polyply/data/ibi/PTMA.CGM3.ibi.ff b/polyply/data/ibi/PTMA.CGM3.ibi.ff index 3f55c420..f6b629ab 100644 --- a/polyply/data/ibi/PTMA.CGM3.ibi.ff +++ b/polyply/data/ibi/PTMA.CGM3.ibi.ff @@ -61,5 +61,5 @@ resname "PTMA" EST VNL +VNL 2 70 20 [ citation ] -2022RAlessandri-arXiv +2023RAlessandri-Macromolecules polyply diff --git a/polyply/data/ibi/citations.bib b/polyply/data/ibi/citations.bib index bc8399e8..1ba4a6f0 100644 --- a/polyply/data/ibi/citations.bib +++ b/polyply/data/ibi/citations.bib @@ -1,13 +1,16 @@ -@article{2022RAlessandri-arXiv, - title={Predicting Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions}, - author={Alessandri, Riccardo and de Pablo, Juan J.}, - journal={arXiv}, - year={2022}, - eprint={2209.02072}, - primaryClass={cond-mat.soft}, - doi={https://doi.org/10.48550/arXiv.2209.02072} + +@article{2023RAlessandri-Macromolecules, + title={Prediction of Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions}, + author={Alessandri, Riccardo and de Pablo, Juan J}, + journal={Macromolecules}, + volume={56}, + number={10}, + pages={3574-3584}, + doi={10.1021/acs.macromol.3c00141}, + year={2023} } + @article{polyply, title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials}, author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J}, From 92d18038ed3141c203f633a8b2999b4e730f95c9 Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Sun, 27 Aug 2023 12:32:56 -0500 Subject: [PATCH 04/11] Add [info] section with links to https://doi.org/10.5281/zenodo.8287521 --- polyply/data/ibi/PTMA.CGM3.ibi.ff | 3 +++ 1 file changed, 3 insertions(+) diff --git a/polyply/data/ibi/PTMA.CGM3.ibi.ff b/polyply/data/ibi/PTMA.CGM3.ibi.ff index f6b629ab..1b8f9070 100644 --- a/polyply/data/ibi/PTMA.CGM3.ibi.ff +++ b/polyply/data/ibi/PTMA.CGM3.ibi.ff @@ -1,6 +1,9 @@ [ moleculetype ] ; name nexcl. PTMA 2 + +[ info ] +Nonbonded interaction potentials (and example run) can be found at: https://doi.org/10.5281/zenodo.8287521 [ atoms ] ; id type resnr residu atom cgnr charge mass From e3480d8d72337c50096c2202c8aa42fb238a7c0a Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Sun, 27 Aug 2023 12:33:53 -0500 Subject: [PATCH 05/11] Rename folder for PTMA CGM3 IBI from ibi/ to ibi_CGM3/ --- polyply/data/{ibi => ibi_CGM3}/PTMA.CGM3.ibi.ff | 0 polyply/data/{ibi => ibi_CGM3}/citations.bib | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename polyply/data/{ibi => ibi_CGM3}/PTMA.CGM3.ibi.ff (100%) rename polyply/data/{ibi => ibi_CGM3}/citations.bib (100%) diff --git a/polyply/data/ibi/PTMA.CGM3.ibi.ff b/polyply/data/ibi_CGM3/PTMA.CGM3.ibi.ff similarity index 100% rename from polyply/data/ibi/PTMA.CGM3.ibi.ff rename to polyply/data/ibi_CGM3/PTMA.CGM3.ibi.ff diff --git a/polyply/data/ibi/citations.bib b/polyply/data/ibi_CGM3/citations.bib similarity index 100% rename from polyply/data/ibi/citations.bib rename to polyply/data/ibi_CGM3/citations.bib From 9fea477ea188699af631a6319fdc07a1e6a2e772 Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Sun, 27 Aug 2023 12:36:08 -0500 Subject: [PATCH 06/11] Add test for ibi_CGM3 PTMA --- .../ibi_CGM3/PTMA/polyply/PTMA.itp | 316 ++++++++++++++++++ .../ibi_CGM3/PTMA/polyply/command | 1 + polyply/tests/test_lib_files.py | 1 + 3 files changed, 318 insertions(+) create mode 100644 polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/PTMA.itp create mode 100644 polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/command diff --git a/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/PTMA.itp b/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/PTMA.itp new file mode 100644 index 00000000..d4883f03 --- /dev/null +++ b/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/PTMA.itp @@ -0,0 +1,316 @@ +; /Users/alessandri/miniconda3/envs/polyplyRA/bin/polyply gen_params -lib ibi_CGM3 -seq PTMA:10 -o PTMA.itp -name PTMA + +; Please cite the following papers: +; Alessandri, R; de Pablo, J J; Macromolecules 2023; 10.1021/acs.macromol.3c00141 +; Grunewald, F; Alessandri, R; Kroon, P C; Monticelli, L; Souza, P C; Marrink, S J; Nature Communications 2022; 10.1038/s41467-021-27627-4 + +[ moleculetype ] +PTMA 2 + +[ atoms ] + 1 VNL 1 PTMA VNL 1 0.0 54.0 + 2 EST 1 PTMA EST 2 0.0 54.0 + 3 C1 1 PTMA C1 3 0.0 54.0 + 4 C2 1 PTMA C2 4 0.0 54.0 + 5 C2 1 PTMA C3 5 0.0 54.0 + 6 N4 1 PTMA N4 6 0.0 36.0 + 7 VNL 2 PTMA VNL 7 0.0 54.0 + 8 EST 2 PTMA EST 8 0.0 54.0 + 9 C1 2 PTMA C1 9 0.0 54.0 +10 C2 2 PTMA C2 10 0.0 54.0 +11 C2 2 PTMA C3 11 0.0 54.0 +12 N4 2 PTMA N4 12 0.0 36.0 +13 VNL 3 PTMA VNL 13 0.0 54.0 +14 EST 3 PTMA EST 14 0.0 54.0 +15 C1 3 PTMA C1 15 0.0 54.0 +16 C2 3 PTMA C2 16 0.0 54.0 +17 C2 3 PTMA C3 17 0.0 54.0 +18 N4 3 PTMA N4 18 0.0 36.0 +19 VNL 4 PTMA VNL 19 0.0 54.0 +20 EST 4 PTMA EST 20 0.0 54.0 +21 C1 4 PTMA C1 21 0.0 54.0 +22 C2 4 PTMA C2 22 0.0 54.0 +23 C2 4 PTMA C3 23 0.0 54.0 +24 N4 4 PTMA N4 24 0.0 36.0 +25 VNL 5 PTMA VNL 25 0.0 54.0 +26 EST 5 PTMA EST 26 0.0 54.0 +27 C1 5 PTMA C1 27 0.0 54.0 +28 C2 5 PTMA C2 28 0.0 54.0 +29 C2 5 PTMA C3 29 0.0 54.0 +30 N4 5 PTMA N4 30 0.0 36.0 +31 VNL 6 PTMA VNL 31 0.0 54.0 +32 EST 6 PTMA EST 32 0.0 54.0 +33 C1 6 PTMA C1 33 0.0 54.0 +34 C2 6 PTMA C2 34 0.0 54.0 +35 C2 6 PTMA C3 35 0.0 54.0 +36 N4 6 PTMA N4 36 0.0 36.0 +37 VNL 7 PTMA VNL 37 0.0 54.0 +38 EST 7 PTMA EST 38 0.0 54.0 +39 C1 7 PTMA C1 39 0.0 54.0 +40 C2 7 PTMA C2 40 0.0 54.0 +41 C2 7 PTMA C3 41 0.0 54.0 +42 N4 7 PTMA N4 42 0.0 36.0 +43 VNL 8 PTMA VNL 43 0.0 54.0 +44 EST 8 PTMA EST 44 0.0 54.0 +45 C1 8 PTMA C1 45 0.0 54.0 +46 C2 8 PTMA C2 46 0.0 54.0 +47 C2 8 PTMA C3 47 0.0 54.0 +48 N4 8 PTMA N4 48 0.0 36.0 +49 VNL 9 PTMA VNL 49 0.0 54.0 +50 EST 9 PTMA EST 50 0.0 54.0 +51 C1 9 PTMA C1 51 0.0 54.0 +52 C2 9 PTMA C2 52 0.0 54.0 +53 C2 9 PTMA C3 53 0.0 54.0 +54 N4 9 PTMA N4 54 0.0 36.0 +55 VNL 10 PTMA VNL 55 0.0 54.0 +56 EST 10 PTMA EST 56 0.0 54.0 +57 C1 10 PTMA C1 57 0.0 54.0 +58 C2 10 PTMA C2 58 0.0 54.0 +59 C2 10 PTMA C3 59 0.0 54.0 +60 N4 10 PTMA N4 60 0.0 36.0 + +[ bonds ] + 1 2 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened + 2 3 1 0.253 15000 ; PMMA-TEMPO connection + 3 4 1 0.326 25000 ; cog (TEMPO) + 3 5 1 0.326 25000 ; cog (TEMPO) + 7 8 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened + 8 9 1 0.253 15000 ; PMMA-TEMPO connection + 9 10 1 0.326 25000 ; cog (TEMPO) + 9 11 1 0.326 25000 ; cog (TEMPO) +13 14 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +14 15 1 0.253 15000 ; PMMA-TEMPO connection +15 16 1 0.326 25000 ; cog (TEMPO) +15 17 1 0.326 25000 ; cog (TEMPO) +19 20 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +20 21 1 0.253 15000 ; PMMA-TEMPO connection +21 22 1 0.326 25000 ; cog (TEMPO) +21 23 1 0.326 25000 ; cog (TEMPO) +25 26 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +26 27 1 0.253 15000 ; PMMA-TEMPO connection +27 28 1 0.326 25000 ; cog (TEMPO) +27 29 1 0.326 25000 ; cog (TEMPO) +31 32 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +32 33 1 0.253 15000 ; PMMA-TEMPO connection +33 34 1 0.326 25000 ; cog (TEMPO) +33 35 1 0.326 25000 ; cog (TEMPO) +37 38 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +38 39 1 0.253 15000 ; PMMA-TEMPO connection +39 40 1 0.326 25000 ; cog (TEMPO) +39 41 1 0.326 25000 ; cog (TEMPO) +43 44 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +44 45 1 0.253 15000 ; PMMA-TEMPO connection +45 46 1 0.326 25000 ; cog (TEMPO) +45 47 1 0.326 25000 ; cog (TEMPO) +49 50 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +50 51 1 0.253 15000 ; PMMA-TEMPO connection +51 52 1 0.326 25000 ; cog (TEMPO) +51 53 1 0.326 25000 ; cog (TEMPO) +55 56 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +56 57 1 0.253 15000 ; PMMA-TEMPO connection +57 58 1 0.326 25000 ; cog (TEMPO) +57 59 1 0.326 25000 ; cog (TEMPO) + +; vinyl backbone + 1 7 1 0.315 4000 + 7 13 1 0.315 4000 +13 19 1 0.315 4000 +19 25 1 0.315 4000 +25 31 1 0.315 4000 +31 37 1 0.315 4000 +37 43 1 0.315 4000 +43 49 1 0.315 4000 +49 55 1 0.315 4000 + +#ifdef FLEXIBLE + 3 6 1 0.310 100000 ; cog (TEMPO) + 4 6 1 0.238 100000 ; cog (TEMPO) + 5 6 1 0.238 100000 ; cog (TEMPO) + 9 12 1 0.310 100000 ; cog (TEMPO) +10 12 1 0.238 100000 ; cog (TEMPO) +11 12 1 0.238 100000 ; cog (TEMPO) +15 18 1 0.310 100000 ; cog (TEMPO) +16 18 1 0.238 100000 ; cog (TEMPO) +17 18 1 0.238 100000 ; cog (TEMPO) +21 24 1 0.310 100000 ; cog (TEMPO) +22 24 1 0.238 100000 ; cog (TEMPO) +23 24 1 0.238 100000 ; cog (TEMPO) +27 30 1 0.310 100000 ; cog (TEMPO) +28 30 1 0.238 100000 ; cog (TEMPO) +29 30 1 0.238 100000 ; cog (TEMPO) +33 36 1 0.310 100000 ; cog (TEMPO) +34 36 1 0.238 100000 ; cog (TEMPO) +35 36 1 0.238 100000 ; cog (TEMPO) +39 42 1 0.310 100000 ; cog (TEMPO) +40 42 1 0.238 100000 ; cog (TEMPO) +41 42 1 0.238 100000 ; cog (TEMPO) +45 48 1 0.310 100000 ; cog (TEMPO) +46 48 1 0.238 100000 ; cog (TEMPO) +47 48 1 0.238 100000 ; cog (TEMPO) +51 54 1 0.310 100000 ; cog (TEMPO) +52 54 1 0.238 100000 ; cog (TEMPO) +53 54 1 0.238 100000 ; cog (TEMPO) +57 60 1 0.310 100000 ; cog (TEMPO) +58 60 1 0.238 100000 ; cog (TEMPO) +59 60 1 0.238 100000 ; cog (TEMPO) +#endif + +[ constraints ] +#ifndef FLEXIBLE + 3 6 1 0.310 ; cog (TEMPO) + 4 6 1 0.238 ; cog (TEMPO) + 5 6 1 0.238 ; cog (TEMPO) + 9 12 1 0.310 ; cog (TEMPO) +10 12 1 0.238 ; cog (TEMPO) +11 12 1 0.238 ; cog (TEMPO) +15 18 1 0.310 ; cog (TEMPO) +16 18 1 0.238 ; cog (TEMPO) +17 18 1 0.238 ; cog (TEMPO) +21 24 1 0.310 ; cog (TEMPO) +22 24 1 0.238 ; cog (TEMPO) +23 24 1 0.238 ; cog (TEMPO) +27 30 1 0.310 ; cog (TEMPO) +28 30 1 0.238 ; cog (TEMPO) +29 30 1 0.238 ; cog (TEMPO) +33 36 1 0.310 ; cog (TEMPO) +34 36 1 0.238 ; cog (TEMPO) +35 36 1 0.238 ; cog (TEMPO) +39 42 1 0.310 ; cog (TEMPO) +40 42 1 0.238 ; cog (TEMPO) +41 42 1 0.238 ; cog (TEMPO) +45 48 1 0.310 ; cog (TEMPO) +46 48 1 0.238 ; cog (TEMPO) +47 48 1 0.238 ; cog (TEMPO) +51 54 1 0.310 ; cog (TEMPO) +52 54 1 0.238 ; cog (TEMPO) +53 54 1 0.238 ; cog (TEMPO) +57 60 1 0.310 ; cog (TEMPO) +58 60 1 0.238 ; cog (TEMPO) +59 60 1 0.238 ; cog (TEMPO) +#endif + +[ angles ] + 1 2 3 2 132.9 70 ; PMMA-TEMPO connection + 2 3 4 2 129.0 60 ; PMMA-TEMPO connection + 2 3 5 2 121.9 95 ; PMMA-TEMPO connection + 7 8 9 2 132.9 70 ; PMMA-TEMPO connection + 8 9 10 2 129.0 60 ; PMMA-TEMPO connection + 8 9 11 2 121.9 95 ; PMMA-TEMPO connection +13 14 15 2 132.9 70 ; PMMA-TEMPO connection +14 15 16 2 129.0 60 ; PMMA-TEMPO connection +14 15 17 2 121.9 95 ; PMMA-TEMPO connection +19 20 21 2 132.9 70 ; PMMA-TEMPO connection +20 21 22 2 129.0 60 ; PMMA-TEMPO connection +20 21 23 2 121.9 95 ; PMMA-TEMPO connection +25 26 27 2 132.9 70 ; PMMA-TEMPO connection +26 27 28 2 129.0 60 ; PMMA-TEMPO connection +26 27 29 2 121.9 95 ; PMMA-TEMPO connection +31 32 33 2 132.9 70 ; PMMA-TEMPO connection +32 33 34 2 129.0 60 ; PMMA-TEMPO connection +32 33 35 2 121.9 95 ; PMMA-TEMPO connection +37 38 39 2 132.9 70 ; PMMA-TEMPO connection +38 39 40 2 129.0 60 ; PMMA-TEMPO connection +38 39 41 2 121.9 95 ; PMMA-TEMPO connection +43 44 45 2 132.9 70 ; PMMA-TEMPO connection +44 45 46 2 129.0 60 ; PMMA-TEMPO connection +44 45 47 2 121.9 95 ; PMMA-TEMPO connection +49 50 51 2 132.9 70 ; PMMA-TEMPO connection +50 51 52 2 129.0 60 ; PMMA-TEMPO connection +50 51 53 2 121.9 95 ; PMMA-TEMPO connection +55 56 57 2 132.9 70 ; PMMA-TEMPO connection +56 57 58 2 129.0 60 ; PMMA-TEMPO connection +56 57 59 2 121.9 95 ; PMMA-TEMPO connection + 2 1 7 2 70 20 + 8 7 13 2 70 20 +14 13 19 2 70 20 +20 19 25 2 70 20 +26 25 31 2 70 20 +32 31 37 2 70 20 +38 37 43 2 70 20 +44 43 49 2 70 20 +50 49 55 2 70 20 + +; vinyl backbone + 1 7 13 2 115 35 + 7 13 19 2 115 35 +13 19 25 2 115 35 +19 25 31 2 115 35 +25 31 37 2 115 35 +31 37 43 2 115 35 +37 43 49 2 115 35 +43 49 55 2 115 35 + +[ dihedrals ] + 3 4 5 6 2 140.00 20 ; cog (TEMPO) + 2 4 5 6 2 150.00 80 ; PMMA-TEMPO connection + 9 10 11 12 2 140.00 20 ; cog (TEMPO) + 8 10 11 12 2 150.00 80 ; PMMA-TEMPO connection +15 16 17 18 2 140.00 20 ; cog (TEMPO) +14 16 17 18 2 150.00 80 ; PMMA-TEMPO connection +21 22 23 24 2 140.00 20 ; cog (TEMPO) +20 22 23 24 2 150.00 80 ; PMMA-TEMPO connection +27 28 29 30 2 140.00 20 ; cog (TEMPO) +26 28 29 30 2 150.00 80 ; PMMA-TEMPO connection +33 34 35 36 2 140.00 20 ; cog (TEMPO) +32 34 35 36 2 150.00 80 ; PMMA-TEMPO connection +39 40 41 42 2 140.00 20 ; cog (TEMPO) +38 40 41 42 2 150.00 80 ; PMMA-TEMPO connection +45 46 47 48 2 140.00 20 ; cog (TEMPO) +44 46 47 48 2 150.00 80 ; PMMA-TEMPO connection +51 52 53 54 2 140.00 20 ; cog (TEMPO) +50 52 53 54 2 150.00 80 ; PMMA-TEMPO connection +57 58 59 60 2 140.00 20 ; cog (TEMPO) +56 58 59 60 2 150.00 80 ; PMMA-TEMPO connection + +[ exclusions ] + 1 2 3 4 5 6 + 2 3 4 5 6 + 3 4 5 6 + 4 5 6 + 5 6 + 7 8 9 10 11 12 + 8 9 10 11 12 + 9 10 11 12 +10 11 12 +11 12 +13 14 15 16 17 18 +14 15 16 17 18 +15 16 17 18 +16 17 18 +17 18 +19 20 21 22 23 24 +20 21 22 23 24 +21 22 23 24 +22 23 24 +23 24 +25 26 27 28 29 30 +26 27 28 29 30 +27 28 29 30 +28 29 30 +29 30 +31 32 33 34 35 36 +32 33 34 35 36 +33 34 35 36 +34 35 36 +35 36 +37 38 39 40 41 42 +38 39 40 41 42 +39 40 41 42 +40 41 42 +41 42 +43 44 45 46 47 48 +44 45 46 47 48 +45 46 47 48 +46 47 48 +47 48 +49 50 51 52 53 54 +50 51 52 53 54 +51 52 53 54 +52 53 54 +53 54 +55 56 57 58 59 60 +56 57 58 59 60 +57 58 59 60 +58 59 60 +59 60 + diff --git a/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/command b/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/command new file mode 100644 index 00000000..d834b0b7 --- /dev/null +++ b/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/command @@ -0,0 +1 @@ +polyply gen_params -lib ibi_CGM3 -seq PTMA:10 -o PTMA.itp -name PTMA diff --git a/polyply/tests/test_lib_files.py b/polyply/tests/test_lib_files.py index 98d748eb..0f169f4f 100644 --- a/polyply/tests/test_lib_files.py +++ b/polyply/tests/test_lib_files.py @@ -188,6 +188,7 @@ def _interaction_equal(interaction1, interaction2, inter_type): ['martini3', 'P3HT'], ['martini3', 'PPE'], ['martini3', 'PTMA'], + ['ibi_CGM3', 'PTMA'], ['martini2', 'PEO'], ['martini2', 'PS'], ['martini2', 'PEL'], From 84bacc663eb2bfe7aa223c8897b9054ea1c842dc Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Sun, 27 Aug 2023 12:39:51 -0500 Subject: [PATCH 07/11] Add PTMA CGM3 IBI to LIBRARY.md --- LIBRARY.md | 1 + 1 file changed, 1 insertion(+) diff --git a/LIBRARY.md b/LIBRARY.md index 9501df49..64976abc 100644 --- a/LIBRARY.md +++ b/LIBRARY.md @@ -22,6 +22,7 @@ | | | |[martini3](polyply/data/martini3/PSS.martini3.ff) | |Poly(para-phenylene ethynylene)|PPE | |[martini3](polyply/data/martini3/PPE.martini3.ff) | |Poly(TEMPO methacrylate) |PTMA | |[martini3](polyply/data/martini3/PTMA.martini3.ff) | +| | | |[ibi_CGM3](polyply/data/ibi_CGM3/PTMA.CGM3.ibi.ff) | |Dextran |DEX | |[martini3](polyply/data/martini3/dextran.martini3.ff) | |DNA nucleobases |Dx, Tx5, Dx3 w/ x=T,G,A,C|[parmbsc1](polyply/data/parmbsc1/dna_final.ff) |[martini2](polyply/data/martini2/DNA_M2.ff) | |Aminoacids |3 letter code | |[martini3](polyply/data/martini3/aminoacids.ff) | From f5a38e8b3ebe9d75a796094d3be8046251e2c86c Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Sun, 27 Aug 2023 12:47:34 -0500 Subject: [PATCH 08/11] News article for the PTMA paper; version=0 --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index d7533250..d774a6d9 100644 --- a/README.md +++ b/README.md @@ -39,6 +39,7 @@ force-field, molecule parameters and this program. - (Feb 8, 22') **Featured Research Article in Nature Communcations.** Our article on the polyply software suite is now featured on the [Editors' Highlights](https://www.nature.com/collections/hhfigaahch) for Structural biology, biochemistry and biophysics in Nature Communications. The Editors’ Highlights pages aims to showcase the 50 best papers recently published in an area. The development team is beyond happy to receive this honor. - (May 23, 22') **Fighting Cancer with polyply.** Dane et al. used polyply to setup simulations of vesicles and lipid nanodiscs (LNDs) containing PEGylated lipids, which are used as nanocarriers for cancer therapeutics. They find that LNDs are more effective in delivery likely due to their higher flexibility. Check it out in [Nature Materials](https://www.nature.com/articles/s41563-022-01251-z). - (Jan 18, 23') **Towards whole cell simulations with polyply.** In [a perspective on whole-cell simulations](https://www.frontiersin.org/articles/10.3389/fchem.2023.1106495/full) using the Martini force field, Stevens *et al.* utilize polyply to construct the full 0.5 Mio bp chromosome of the Syn3A minimal cell. This impressive task is a good example of the power of the upcoming DNA implementation into polyply and the role of polyply in the Martini Ecosystem. +- (May 11, 23') **Electronic coarse-grained models in polyply.** Curious about simulating non-conjugated radical-containing polymers for all-organic batteries? The models developed [in this work](https://doi.org/10.1021/acs.macromol.3c00141) for the poly(TEMPO acrylamide), or PTMA, are avaiable in polyply. There is an all-atom model, and different coarse-grained model (Martini 3, iterative Boltzmann inversion), all of which can be flexibly handled by polyply. ## Contributions & Support We are happy to accept submissions of polymer parameters to the polyply library. To submit parameters simply From ba33d57794838a3ebcf1afd6384238e02a0d376a Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Sun, 27 Aug 2023 12:49:30 -0500 Subject: [PATCH 09/11] News article for the PTMA paper; version=0.1 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d774a6d9..7dab01bd 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ force-field, molecule parameters and this program. - (Feb 8, 22') **Featured Research Article in Nature Communcations.** Our article on the polyply software suite is now featured on the [Editors' Highlights](https://www.nature.com/collections/hhfigaahch) for Structural biology, biochemistry and biophysics in Nature Communications. The Editors’ Highlights pages aims to showcase the 50 best papers recently published in an area. The development team is beyond happy to receive this honor. - (May 23, 22') **Fighting Cancer with polyply.** Dane et al. used polyply to setup simulations of vesicles and lipid nanodiscs (LNDs) containing PEGylated lipids, which are used as nanocarriers for cancer therapeutics. They find that LNDs are more effective in delivery likely due to their higher flexibility. Check it out in [Nature Materials](https://www.nature.com/articles/s41563-022-01251-z). - (Jan 18, 23') **Towards whole cell simulations with polyply.** In [a perspective on whole-cell simulations](https://www.frontiersin.org/articles/10.3389/fchem.2023.1106495/full) using the Martini force field, Stevens *et al.* utilize polyply to construct the full 0.5 Mio bp chromosome of the Syn3A minimal cell. This impressive task is a good example of the power of the upcoming DNA implementation into polyply and the role of polyply in the Martini Ecosystem. -- (May 11, 23') **Electronic coarse-grained models in polyply.** Curious about simulating non-conjugated radical-containing polymers for all-organic batteries? The models developed [in this work](https://doi.org/10.1021/acs.macromol.3c00141) for the poly(TEMPO acrylamide), or PTMA, are avaiable in polyply. There is an all-atom model, and different coarse-grained model (Martini 3, iterative Boltzmann inversion), all of which can be flexibly handled by polyply. +- (May 11, 23') **Electronic coarse-grained models in polyply.** Curious about simulating non-conjugated radical-containing polymers for all-organic batteries? The models developed [in this work](https://doi.org/10.1021/acs.macromol.3c00141) for PTMA, or poly(TEMPO acrylamide), are avaiable in polyply. There is an all-atom model and different coarse-grained model (Martini 3, iterative Boltzmann inversion), all of which can be flexibly handled by polyply. ## Contributions & Support We are happy to accept submissions of polymer parameters to the polyply library. To submit parameters simply From 9878b82ff651acefb2062f549fa23eb519f4a8c3 Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Fri, 13 Oct 2023 11:00:51 -0500 Subject: [PATCH 10/11] Rename ibi_CGM3 to ibi_cgm3 (lower-case) --- LIBRARY.md | 2 +- .../{ibi_CGM3/PTMA.CGM3.ibi.ff => ibi_cgm3/PTMA.cgm3.ibi.ff} | 0 polyply/data/{ibi_CGM3 => ibi_cgm3}/citations.bib | 0 .../tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/command | 1 - .../library_tests/{ibi_CGM3 => ibi_cgm3}/PTMA/polyply/PTMA.itp | 2 +- .../tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/command | 1 + polyply/tests/test_lib_files.py | 2 +- 7 files changed, 4 insertions(+), 4 deletions(-) rename polyply/data/{ibi_CGM3/PTMA.CGM3.ibi.ff => ibi_cgm3/PTMA.cgm3.ibi.ff} (100%) rename polyply/data/{ibi_CGM3 => ibi_cgm3}/citations.bib (100%) delete mode 100644 polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/command rename polyply/tests/test_data/library_tests/{ibi_CGM3 => ibi_cgm3}/PTMA/polyply/PTMA.itp (99%) create mode 100644 polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/command diff --git a/LIBRARY.md b/LIBRARY.md index 64976abc..e08303b2 100644 --- a/LIBRARY.md +++ b/LIBRARY.md @@ -22,7 +22,7 @@ | | | |[martini3](polyply/data/martini3/PSS.martini3.ff) | |Poly(para-phenylene ethynylene)|PPE | |[martini3](polyply/data/martini3/PPE.martini3.ff) | |Poly(TEMPO methacrylate) |PTMA | |[martini3](polyply/data/martini3/PTMA.martini3.ff) | -| | | |[ibi_CGM3](polyply/data/ibi_CGM3/PTMA.CGM3.ibi.ff) | +| | | |[ibi_cgm3](polyply/data/ibi_cmg3/PTMA.cgm3.ibi.ff) | |Dextran |DEX | |[martini3](polyply/data/martini3/dextran.martini3.ff) | |DNA nucleobases |Dx, Tx5, Dx3 w/ x=T,G,A,C|[parmbsc1](polyply/data/parmbsc1/dna_final.ff) |[martini2](polyply/data/martini2/DNA_M2.ff) | |Aminoacids |3 letter code | |[martini3](polyply/data/martini3/aminoacids.ff) | diff --git a/polyply/data/ibi_CGM3/PTMA.CGM3.ibi.ff b/polyply/data/ibi_cgm3/PTMA.cgm3.ibi.ff similarity index 100% rename from polyply/data/ibi_CGM3/PTMA.CGM3.ibi.ff rename to polyply/data/ibi_cgm3/PTMA.cgm3.ibi.ff diff --git a/polyply/data/ibi_CGM3/citations.bib b/polyply/data/ibi_cgm3/citations.bib similarity index 100% rename from polyply/data/ibi_CGM3/citations.bib rename to polyply/data/ibi_cgm3/citations.bib diff --git a/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/command b/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/command deleted file mode 100644 index d834b0b7..00000000 --- a/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/command +++ /dev/null @@ -1 +0,0 @@ -polyply gen_params -lib ibi_CGM3 -seq PTMA:10 -o PTMA.itp -name PTMA diff --git a/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/PTMA.itp b/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/PTMA.itp similarity index 99% rename from polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/PTMA.itp rename to polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/PTMA.itp index d4883f03..1e31b986 100644 --- a/polyply/tests/test_data/library_tests/ibi_CGM3/PTMA/polyply/PTMA.itp +++ b/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/PTMA.itp @@ -1,4 +1,4 @@ -; /Users/alessandri/miniconda3/envs/polyplyRA/bin/polyply gen_params -lib ibi_CGM3 -seq PTMA:10 -o PTMA.itp -name PTMA +; /Users/alessandri/miniconda3/envs/polyplyRA/bin/polyply gen_params -lib ibi_cgm3 -seq PTMA:10 -o PTMA.itp -name PTMA ; Please cite the following papers: ; Alessandri, R; de Pablo, J J; Macromolecules 2023; 10.1021/acs.macromol.3c00141 diff --git a/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/command b/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/command new file mode 100644 index 00000000..7cfea0c6 --- /dev/null +++ b/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/command @@ -0,0 +1 @@ +polyply gen_params -lib ibi_cgm3 -seq PTMA:10 -o PTMA.itp -name PTMA diff --git a/polyply/tests/test_lib_files.py b/polyply/tests/test_lib_files.py index 0f169f4f..849c7b73 100644 --- a/polyply/tests/test_lib_files.py +++ b/polyply/tests/test_lib_files.py @@ -188,7 +188,7 @@ def _interaction_equal(interaction1, interaction2, inter_type): ['martini3', 'P3HT'], ['martini3', 'PPE'], ['martini3', 'PTMA'], - ['ibi_CGM3', 'PTMA'], + ['ibi_cgm3', 'PTMA'], ['martini2', 'PEO'], ['martini2', 'PS'], ['martini2', 'PEL'], From 424a5117f9a5518949110ff20f1038effa4ea7d2 Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Fri, 13 Oct 2023 11:09:20 -0500 Subject: [PATCH 11/11] Remove extra paranthesis from line in LIBRARY.md --- LIBRARY.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LIBRARY.md b/LIBRARY.md index 7af5f67f..b5d3a01f 100644 --- a/LIBRARY.md +++ b/LIBRARY.md @@ -21,7 +21,7 @@ |Polystyrene sulfonate |PSS | |[martini2](polyply/data/martini2/PSS.martini.2.itp) | | | | |[martini3](polyply/data/martini3/PSS.martini3.ff) | |Poly(para-phenylene ethynylene)|PPE | |[martini3](polyply/data/martini3/PPE.martini3.ff) | -|Poly(TEMPO methacrylate) |PTMA |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PTMA.oplsaa.LigParGen.ff)]|[martini3](polyply/data/martini3/PTMA.martini3.ff) | +|Poly(TEMPO methacrylate) |PTMA |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PTMA.oplsaa.LigParGen.ff)|[martini3](polyply/data/martini3/PTMA.martini3.ff) | | | | |[ibi_cgm3](polyply/data/ibi_cmg3/PTMA.cgm3.ibi.ff) | |Dextran |DEX | |[martini3](polyply/data/martini3/dextran.martini3.ff) | |DNA nucleobases |Dx, Tx5, Dx3 w/ x=T,G,A,C|[parmbsc1](polyply/data/parmbsc1/dna_final.ff) |[martini2](polyply/data/martini2/DNA_M2.ff) |