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

Piggot T. T.Piggot at soton.ac.uk
Tue May 19 13:47:54 CEST 2015

Ah, cool. I had misread that Chris was saying shift rather than switch in parts of his previous email. Good to know that force switching can also be achieved in GROMACS versions prior to 5.



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: 19 May 2015 12:39
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7

On 5/19/15 5:37 AM, Piggot T. wrote:
> 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.

While it is reasonably safe to say that we know of no problems for protein and
nucleic acid force fields with potential switching in homogeneous media, that's
as far as I can say.  Those force fields are a bit more robust in their response
to nonbonded treatment.  The lipid force field in general (not just DPPC) is
very sensitive, and as you note, and needs to be used exactly as prescribed.

Note, though, that force-switching has in fact been in GROMACS for quite some
time, with vdwtype = shift.  NAMD introduced force-switching around the time
that the CHARMM default became vfswitch (2010); old versions of the (additive)
force field defaulted to vswitch (potential-switching) but vfswitch is the
standard now for CHARMM36.



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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