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

[Christopher Neale]

Thank you Justin, Tom, and Mark for all of this advice.

I will let you know what I find.

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 Mark Abraham <mark.j.abraham at gmail.com>
Sent: 19 May 2015 08:44
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7

Hi

On Tue, May 19, 2015 at 5:35 AM Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> 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.


Naturally, that's your decision :-) But I hope that people in general
adopting that strategy at least try out and compare newer versions of the
code for their simulations, even if they don't plan to publish with those
versions. The combinatorics of MD validation make centralized testing
prohibitively expensive (though there are some plans that might get funded
some time...), so if there's a problem that only shows up for an individual
user, then it could stay unnoticed for a long time, and that's clearly not
in your long term interests. (And you might decide the improved performance
enhances your sampling enough to accept what may be higher bug risk...)
Hardware and software enhancements will eventually force people to use
newer software versions, and both kinds of enhancements are happening
exponentially fast at the moment...

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.
>

I would strongly encourage that kind of testing - use mdrun -rerun to
compare forces and energies to complement reading docs and asking people.
Code doesn't lie (much)

Mark


> 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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