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

From: Arun Srikanth via AMBER <amber.ambermd.org>
Date: Fri, 26 May 2023 19:47:11 +0200

Hi Eddie

You need to apply dispersion corrections for energy and pressure. For
pressure the correction cannot be neglected
More on this you can find here
https://manual.gromacs.org/current/reference-manual/functions/long-range-vdw.html
Arun

On Fri, May 26, 2023 at 7:05 PM Eduard Neu via AMBER <amber.ambermd.org>
wrote:

> 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 - 11:00:03 PDT