[AMBER] mdp parameters when using the AMBER force field with GROMACS

From: Eduard Neu via AMBER <amber.ambermd.org>
Date: Fri, 26 May 2023 18:57:44 +0200

Hi everyone,

I also posted this question in the GROAMCS forum, but haven’t received a
satisfying answer yet:

https://gromacs.bioexcel.eu/t/mdp-parameters-for-non-bonded-interaction-using-the-amber-force-field/6458

In the GROMACS manual there are no clear recommendation regarding the
non-bonded parameters when using the AMBER force field:

https://gromacs.bioexcel.eu/t/mdp-parameters-for-non-bonded-interaction-using-the-amber-force-field/6458

I came across this post:

https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/9

in which following parameters are recommended:

constraints = h-bonds
rcoulomb = 1.0
rvdw = 1.0
vdw-modifier = Potential-shift-Verlet
DispCorr = EnerPres
coulombtype = PME
fourierspacing = 0.125

Based on how ff19SB and lipid21 were tested a cutoff of 10 Åis reasonable.

However, I don’t understand why vdw-modifier = Potential-shift-Verlet
and DisCorr = EnerPress is used.

Is there any literature on this available or am I missing something out
in the original publications of the force fields?

Additionally, CHARMM-GUI generated outputs that use vdw-modifier = None.

Regard
Eddie
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Received on Fri May 26 2023 - 10:00:02 PDT