GROMACS version: GROMACS modification: Yes/No Hi all. I want to ask about the functionality of the “deform” option in different versions. The system I am studying consist of pure isotactic polypropylene at the united atom level and I am deforming the box uniaxially along the x direction (the mdp file is attached). In the past, I was using GROMACS 2020 and everything was runnin…

GROMACS version: GROMACS modification: Yes/No Here post your question I am working on the CG Simulations with large systems. During PBC definition I used gmx edifconf -f -bt cubic -d 1.0 -o tried this and also increased the box size 60 60 60. Then during ionisation, it showed an error which I have attached with the mail. I tried to solve this error by increasing the…

GROMACS version: 2023 GROMACS modification: No This is somewhat a trivial matter but would it be complicated to make OPC an optional enum option inside of gmx pdb2gmx? I’m often relying on workflows to automate system preparation, and the only thing that I have to do manually is to interactively select the water model, because --water opc is not a legal choice (even though the .f…

GROMACS version: 2021.4 GROMACS modification: Yes/No Here post your question : I want to simulate my system at different temperature, say 290K. So I have to change the ref_t from 300K to 290K in nvt.mdp, npt.mdp and md.mdp files. In the nvt.mdp, do I need to change the gen_t (Maxwell distribution) to 290K too? The following is the nvt.mdp file- title = charmm36 CYHE N…