Merge branch 'master' into PTMA-GBNO2-IBI-ff

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                     |[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)    |
 |                               |                         |                                                                       |[ibi_gbcg](polyply/data/ibi_gbcg/PTMA.gbno2.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)           |

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 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 

polyply/data/ibi_cgm3/PTMA.cgm3.ibi.ff

@@ -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

polyply/data/ibi_cgm3/citations.bib

@@ -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}
+}