GROMACS version: version 2018.1 GROMACS modification: Yes/No Here post your question I am getting the following error while running gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry ‘title’ NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is >= 10,…

GROMACS version: 5.1.4 GROMACS modification: Yes Dear Gromacs users, I am working on the preparation of modified starch by substituting a cationic group on amylose and amylopectin chains. To generate the topology of modified chains by pdb2gmx command, I need to add the substituted cation residue type in .rtp file for which I need the charge on atoms of cation and the changed cha…

GROMACS version:2019.1, 2018.2 GROMACS modification: No Here post your question Friends, I have a multi species system trajectory (memb protein). I want to know, how many times a pair of atoms or a a pair of two molecules/residues come into contact, bond, non-bond interact (#update: I saw Justin has recommended gmx_mindist for contact count) how long (time) these contac…

GROMACS version: 2021.3 GROMACS modification: No Hello, I see that gmx chi allows for the caluclation of a set of J-coupling constants and chemical shifts. The output provides a citation for the methods for calculating the chemical shifts but not one for the Karplus parameters used. I have found the values used in gromacs in the old mailing list archive ([gmx-users] definition o…

GROMACS version:2022 GROMACS modification:No Hello all, I am having trouble converting my modified residue to rtp format. I methylated my residue ATOM 781 N ARG A 130 8.714 54.987 2.676 1.00 47.63 N ATOM 782 CA ARG A 130 9.061 56.391 2.868 1.00 47.63 C ATOM 783 C ARG A 130 9.052 57.092 1.516 1.00 47.63 …