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alanwilter / acpype

OFFICIAL: AnteChamber PYthon Parser interfacE
https://alanwilter.github.io/acpype/
GNU General Public License v3.0
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A question about the content of md.mdp file #94

Closed darekb94 closed 1 year ago

darekb94 commented 1 year ago

ACPYPE script generates, among others, a file md.mdp containg the parameters for testing GROMACS. It contains, for example, force-switching function for van der Waals interactions, as well as the cut-off for PME:

vdw-modifier = force-switch rlist = 1.0 rvdw = 1.0 rvdw-switch = 0.9 rcoulomb = 1.1

A similar treatment was recommended for CHARMM36 force field, however the cut-off distances were slightly different. Therefore, I wonder if there is some kind of recommendation to use this particular cut-offs written in the file md.mdp, or there is a freedom in choosing cut-offs suing General Amber Force Field?

alanwilter commented 1 year ago

No, I can't recommend these parameters, they were chosen just to make it work for a quick test, because there's no solvent. This is just to "check" if the topology generated "behaves" under a simulation in vacuum; GMX removed the proper vacuum functionality, so these parameters would not be even there if we had the vacuum option like we had before.