GROMACS version:2021 GROMACS modification: Yes/No Dear GROMACS users, I am currently trying to simulate a protein-ligand system using the charmm36-jul2021 force field. In the energy minimization step, a large number of pdb files are being generated which majorly contain the solvent (water) molecules. I wonder how these files can be used. Apart from this, the Fmax is not conver…

GROMACS version: 5.1.2 GROMACS modification: Yes/No Here post your question Hi everyone, I want to calculate free energy g_mmpbs 5.1.x. I had MDS in gromacs 2020.1 then I used gromacs 5.1.2 to re generate index.ndx and md.tpr I used these commands: gmx make_ndx -f em.gro -o index1.ndx 1 | 13 q gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index1.ndx -o md_0_1…