[gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7
chris.neale at alum.utoronto.ca
Tue May 19 05:34:35 CEST 2015
Thank you for the suggestion. I don't use gromacs 5 because of things like this: http://redmine.gromacs.org/issues/1603 that tend to pop up early in a release series. Until I needed to run charmm simulations, I use 4.6.7 because it works and I am confident in it. But your suggestion is really good... use gmx 5 to get energies to test against gmx 4 and see if I can find valid settings.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 18 May 2015 20:29
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7
On 5/18/15 2:21 PM, Christopher Neale wrote:
> Dear Users:
> I would like to use the charmm27 force field in gromacs version 4.6.7 and I would like to know if it is possible to get the proper treatment of vdw interactions.
> Information for gromacs 5 is here:
> However, Gromacs 4.6.7 does not contain the option for vdw-modifier = force-switch
> Invalid enum 'force-switch' for variable vdw-modifier, using
> Next time use one of: 'Potential-shift-Verlet' 'Potential-shift' 'None'
> 'Potential-switch' 'Exact-cutoff'
> Is a potential-shift the same as a force-switch and therefore the following options are correct for charmm27 in gromacs 4.6.7?
> ns_type = grid
> cutoff-scheme = verlet
> vdwtype = cut-off
> rlist = 1.2
> rvdw = 1.2
> rvdw-switch = 1.0
> rcoulomb = 1.2
> vdw-modifier = Potential-shift-Verlet
> coulombtype = PME
> I know this has been discussed before on the list, but I can't find anything that seems authoritative for gromacs versions prior to v5.
I cannot personally attest to anything aside from what's on the wiki. We have
verified the forces are equivalent between CHARMM's vfswitch and GROMACS'
force-switch modifier. This is how we do all our simulations, so for posterity,
what I wrote on the wiki is what I must emphasize is known to be correct.
From the manual, it seems that the group scheme + vdwtype = shift is equivalent
to the modern force-switch modifier. The language of potential-shift does not
sound as if it is the same as force-switch, and I don't know why such redundancy
would be present anyway; perhaps legacy naming reasons.
Any reason why you can't use 5.0 with the known correct settings? The check I
would do is a single-point energy with the settings you think are equivalent and
want to test and print out the forces with gmx traj.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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