I'm using Gromacs 2020 to run a protein ligand simulation using Amber99SB for protein and Amber (GAFF) for ligand, in the mdp files should rlist be of the same number as rcoulomb and rvdw e.g. in case of Amber ff , should it too be set to =1.0?
I've read that the cutoffs are specific for each force filed, and that in Amber FF it's about 1.0, and in CHARMM about 1.2, am I getting it right? And if anyone can provide me with a reference for those cutoff values and parameters used in mdp files other than the gromacs manual itself, I'd be grateful.
Thanks in advance
Ricardo J Ferreira
Hi,
you can set it to 1.2... current versions of GROMACS will adjust the radius to best performance when running MD using GPUs.
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