GROMACS version:2019.04 GROMACS modification: No I calculate GROMACS on the supercomputer. The configuration is 64vcpu + 8 * V100 32g How do I allocate resources to achieve the best balance? I tried to calculate with 1 core + 1gpu, which is not very good 1 post - 1 participant Read full topic

I wonder if in latest Gromacs the [pairs] section of the topology file is still used or if Gromacs figures out close by atoms automatically. Gromacs seems to consider non bonded pair interactions between atoms of one molecule even when these are not given in the [pars] section of the toplogy file, so I wonder what is special about those pairs given in the [pairs] section. Is the [p…

GROMACS version: 2021.2 GROMACS modification: Yes - PLUMED patched I have been running the Umbrella sampling tutorial of Justin Lemkul. I could see however that the performance is relatively low compared to what is supposed to be expected by using GPUs. I used a simple workstation with 3 GPUs available. Any ideas how to improve it? I read there are some variables that need to be …

GROMACS version: 2019.6 GROMACS modification: No Here post your question I am running the command “gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr” I am getting the following error ““Fatal error: There was 1 error in input file(s)”” because of this error " ERROR 1 [file inhib1.itp, line 81]: Duplicate atom index (1) in virtual_sites3 " in my itp file: [ vir…