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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,68 @@ | ||
[ 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 | ||
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 ] | ||
2023RAlessandri-Macromolecules | ||
polyply |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,22 @@ | ||
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||
@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}, | ||
journal={Nature Communications}, | ||
doi={10.1038/s41467-021-27627-4}, | ||
year={2022}, | ||
volume={13}, | ||
pages={68} | ||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,75 @@ | ||
[ 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 | ||
1 VNL 1 PTMA VNL 1 0 71.099 | ||
2 EST 1 PTMA EST 2 0 29.018 | ||
3 C1 1 PTMA C1 3 0 56.108 | ||
4 U 1 PTMA NN 4 0 0.000 | ||
5 U 1 PTMA OO 5 0 0.000 | ||
6 C1 1 PTMA C2 6 0 56.108 | ||
7 NO 1 PTMA NO 7 0 30.006 | ||
|
||
[ bonds ] | ||
; i j funct length | ||
1 2 1 0.35337 12500 | ||
2 3 1 0.32325 32000 | ||
2 6 1 0.32369 32000 | ||
3 6 1 0.38838 32000 | ||
3 7 1 0.23794 1000000 {"ifdef": "FLEXIBLE"} | ||
6 7 1 0.23793 1000000 {"ifdef": "FLEXIBLE"} | ||
|
||
[constraints] | ||
; i j funct length | ||
3 7 1 0.23794 {"ifndef": "FLEXIBLE"} | ||
6 7 1 0.23793 {"ifndef": "FLEXIBLE"} | ||
|
||
[ angles ] | ||
; i j k funct length force k | ||
1 2 3 2 130.000 90 | ||
1 2 6 2 130.000 75 | ||
|
||
[dihedrals] | ||
; i j k l funct ref.angle force_k | ||
1 3 6 7 2 165.98 50 | ||
2 3 6 7 2 179.20 80 | ||
3 7 5 6 2 170.723 50 | ||
|
||
[virtual_sites3] | ||
; 3fd sites | ||
; site positioned as a linear combination of 3 atoms; the site is in the same plane | ||
; site from funct a b | ||
4 3 2 7 2 0.834 0.210 | ||
5 3 2 7 2 1.180 0.276 | ||
|
||
[exclusions] | ||
1 2 3 4 5 6 7 | ||
2 3 4 5 6 7 | ||
3 4 5 6 7 | ||
4 5 6 7 | ||
5 6 7 | ||
6 7 | ||
|
||
[ link ] | ||
resname "PTMA" | ||
[ bonds ] | ||
VNL +VNL 1 0.305 12000 {"group": "vinyl backbone"} | ||
|
||
[ link ] | ||
resname "PTMA" | ||
[ angles ] | ||
VNL +VNL ++VNL 2 126 40 {"group": "vinyl backbone"} | ||
|
||
[ link ] | ||
resname "PTMA" | ||
[ angles ] | ||
EST VNL +VNL 2 90 20 | ||
|
||
[ citation ] | ||
2023RAlessandri-Macromolecules | ||
polyply |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,22 @@ | ||
|
||
@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}, | ||
journal={Nature Communications}, | ||
doi={10.1038/s41467-021-27627-4}, | ||
year={2022}, | ||
volume={13}, | ||
pages={68} | ||
} |
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