The various operations of GROMACS

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GROMACS version:2021.5
GROMACS modification: No

Sorry for my poor English.
Please lend me your help, everyone.

I have three questions for you.

①I would like to use the “AMBER” force field to flow the structure of the covalent linkage between sugar and protein with “GROMACS”. I’m thinking of using “CHARMM-GUI”, but what are the bonds, angles, and torsions that contain covalently bonded atoms? In other words, is it derived from either ff14SB or GLYCAM-06j?

②Next, I already finished MD and have each output file. what if I want to add 50ns?

③I would like to reproduce the binding of the ligand to the RNA at 1 μs MD, but I think it would be very difficult in a normal setup. Any suggestions on how to do this?

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Hi,

“②Next, I already finished MD and have each output file. what if I want to add 50ns?”

To extend your GROMACS simulation, you can use gmx convert-tpr to edit your tpr file. see more details how it works here to https://manual.gromacs.org/documentation/current/user-guide/ → Extending a .tpr file

\Alessandra