GROMACS version: 2021.3 GROMACS modification: No I have been trying to minimize the energy of a coarse-grained MARTINI ion channel- membrane system that I constructed with the CHARMM membrane GUI builder. I keep running into the following error even though I have increased rvdw/rcoulomb from 1.1 to 2 and increased nstlist from 20 to 40. I even tried increasing rvdw/rcoulomb from …

GROMACS version: 2022.2 GROMACS modification: Yes/No Here post your question I am trying to pull one atom(Al20) out of a large crystalline structure(MOF_Al20, without atom Al20). Step 1- pull the atom and get configurations Pull code pull = yes pull_ncoords = 1 pull_ngroups = 2 pull_group1_name = Al20 pull_group2_name …

GROMACS version: 2021.4 GROMACS modification: Yes Hello everyone, I was trying to run Gromacs (patched with plumed 2.8) on GPU, but I am noticing that using GPU for calculations is actually reducing performance when compared to running the simulation on CPU only. The configuration of my computer is: CPU: AMD Threadripper PRO 3975WX GPU: RTX A4000 GCC version: 11.2 CUDA vers…