[gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7

[Piggot T.]

Hi Chris,

As far as I understand it, before GROMACS 5 the potential rather than the force was switched off. Since GROMACS 5 you can choose between the two.

As for the settings to use with the CHARMM force field, the CHARMM package itself (as Justin has said) uses force switching. However, in NAMD vdw force switching has only implemented from versions 2.7b3 onwards. For proteins, I cannot see this choice having a large impact as the paper implementing the CHARMM force field in GROMACS (Bjelkmar et al.) will have used the potential switch and all the simulation in NAMD prior to version 2.7b3 will have also used this approach. The one case in which I saw this choice having a large impact was for CHARMM36 membranes and when a combination of normal TIP3P and potential switch was used. When combining these two, this resulted in DPPC membranes transitioning to a gel phase at 323K. If either of these was changed (i.e. if either CHARMM TIP3P/TIPS3P was used or the forces were switched off) the membranes behaved well.

So I would say that if you are using GROMACS prior to version 5 it should be fine (with the CHARMM TIP3P water, especially if using CHARMM36 DPPC membranes) but it is worth bearing in mind that this is slightly different to how it is done in the CHARMM package. Once again, this is just my understanding of the way it has worked in GROMACS versions. One of the developers who implemented the switch cut-offs (Berk?) should be able to confirm (or deny!) this.

Cheers

Tom

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Christopher Neale [chris.neale at alum.utoronto.ca]
Sent: 19 May 2015 04:20
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7

Dear Justin:

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.

Thank you,
Chris.

________________________________________
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:
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> However, Gromacs 4.6.7 does not contain the option for vdw-modifier = force-switch
>
>    Invalid enum 'force-switch' for variable vdw-modifier, using
>    'Potential-shift-Verlet'
>    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

--
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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