GROMACS version: 2021.3 GROMACS modification: No Hi, I’m trying to follow a paper where they’ve carried out simulations using LAMMPS, where they introduce Gaussian potentials with a specified width and depth, at fixed positions. Is there a way to implement something like this in GROMACS? In essence this is required to hold the atoms in place. I know you can use position restraint…

GROMACS version: 2022.5 Related software: ACPYPE, Ambertools22, Gaussian16 The protein I am interested in is PDB:6B6G. There is a 2Fe-2S cluster locating at the center of the protein and the two ion atoms interact with two deprotonated CYS repectively. I already get some parameters from literature and DFT calculation related to the 2Fe2S - 4CYS. Now I would like to embed these b…

GROMACS version: 2020.1-Ubuntu-2020.1-1 GROMACS modification: Yes/No Here post your question: Fatal error: Atom CG in residue VAL 3 was not found in rtp entry VAL with 16 atoms while sorting atoms. 1 post - 1 participant Read full topic

GROMACS version: 2018 GROMACS modification: Yes/No My MD studies are based on CHARMM force field. I want to generate topology parameter file for a molecule using ATB server. How can I select the files that suites for the all atom force field CHARMM. I uploaded the PDB file of the molecule and as mentioned in protein data bank for the net charge of the molecule, the value was giv…

GROMACS version: 2023 GROMACS modification: No I am building GROMACS to run on a single compute node with four GPUs, and I would like to offload PP work to two of the GPUs and PME work to the two. From the installation guide, it’s not clear to me whether CUDA-aware MPI is necessary to allow direct GPU communication on a single node. In the “MPI support” section it says that no u…