GROMACS version: 2020.4
GROMACS modification: No, except for ligand definition.
I’m trying to run MD simulation of a protein/ligand complex using amber99sb or amber14sb FF.
I’ve followed Justin Lemkul’s tutorial (many thanks) adjusting it to amber, but I do have a question about the production md.mdp file.
Is this md.mdp file from the tutorial OK for amber FF or in contrary specific for the CHARMM36 ff (used in the tutorial) ?
I’ve noticed this in the md.mdp file :
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no
Should I use" DispCorr = EnerPres" for amber FF or any other entry ?
Is there any other parameter in the md.mdp file that I should modify to best fit for amber FF ?
Many thanks for your feedback