polyply_1.0

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all atomic block copolymer building

19

Thank you for creating such a wonderful toolkit. Trying to build an all atomic block copolymer model for GROMACS. Thought it should be available with the '-connect' function with the...

WeixZeng

Contributing an OPLS/CM1A model for PS. This PR should wait for https://github.com/marrink-lab/polyply_1.0/pull/327. In the meantime, it is useful for https://github.com/marrink-lab/polyply_1.0/issues/355.

ricalessandri

Contributing an OPLS/CM1A model for PMMA. This PR should wait for https://github.com/marrink-lab/polyply_1.0/pull/327. In the meantime, it is useful for https://github.com/marrink-lab/polyply_1.0/issues/355.

ricalessandri

All atom force field file generation

4

Hello, Thank you for your great software and helpful issue responses. I am having trouble generating a valid .ff file for an all-atom model of nitrile butadiene, acrylonitrile-butadiene copolymer. I...

saabirpetker

Amylose parameters

8

Hi all, I've been using polyply with Martini 3 parameters to create some simulation systems of variable length line polymer solutions. I'm happy to say that CEL and DEX parameters...

JakaBrklanje

Sang nanoparticle

8

Apologies for the delay. Have been rather busy lately. Created first version of the nanoparticle generator. Some notes: - I've made a PCBM-fullerene nanoparticle with it that adapts a custom...

MDSYN2019

[4] Implement frame based backmapping

5

In this pull request, the frame-based backmapping protocol's first version will be implemented. The most basic idea is that users provide internal reference frames for each residue, which will be...

jan-stevens

BUG: branched dextran no longer possible to produce directly

1

Working on latest `master` branch of `polyply`. I was trying to roughly follow the tutorial at https://github.com/marrink-lab/polyply_regression_tests/blob/main/examples/liquid_liquid_phase_separation/PolyplyTutorial.ipynb Then, I noticed that `dextran.martini3.ff` doesn't even have alpha 1->3 linkages anymore, they...

tylerjereddy

**Describe the bug** Using the -split flag causes a renumbering of all resid. However, the resid start at 0 instead of 1. **Command line arguments** Concerns all commands with ```...

fgrunewald

fix issue 285

3

@csbrasnett this is a clean PR with all changes we did yesterday. I also fixed the template generation issue. Can you test this branch? To Do - [x] add test...

fgrunewald