GROMACS version: 2021.4 GROMACS modification: Yes/No I am a newbie in molecular dynamics area. I am following Tutorial 5 of the official Gromacs MD Tutorials. I am trying to generate ligand topology file through GGENFF by following the exact method stated in the tutorial only to get high penalty score (186). I am confused how to proceed further. Please guide me. 1 p…

GROMACS version: 2022 GROMACS modification: No Dear gmx-ers: I have a system consisting of water as well as a number of lipid molecules, which are initially randomly dispersed in the solvent. As the simulation progresses, I want to use gmx select to select those molecules that have either i) started to aggregate or ii) still are in a dispered state. I tried the following syntax…

GROMACS version: 5.1.4 GROMACS modification: No Here post your question: I have a slab geometry with silicon walls, SPC/E water, and potassium chloride. To add the ion-ion and ion-O pairs to CHARMM36 force field, I am planning to apply the parameters from J. Phys. Chem. B 1998, 102, 21, 4193–4204 (https://doi.org/10.1021/jp980642x). I wonder if I can directly use the position of…

GROMACS version: 2023.3 GROMACS modification: Yes (plumed-2.10-dev) Dear all, I have posted this in the plumed mailing list too, as I’m not sure on what end the problem is. I recently found a library that may be useful to (somewhat) easily port certain operations to the GPU . The library is called Bandicoot (Bandicoot download | SourceForge.net) and it does work more or less str…