[gmx-users] Using CHARMM36 in GROMACS
jalemkul at vt.edu
Thu Mar 31 01:11:39 CEST 2016
On 3/30/16 5:17 PM, Gregory Poon wrote:
> Hello everyone,
> I am learning how to perform dynamics on double-stranded DNA sequences using the
> CHARMM36 FF I downloaded from the MacKerell lab. I have consulted the GROMACS
> documentation page regarding specific settings in the .mdp file for CHARMM36
> (http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM), and
> adopted those for the energy minimization step. In these settings, constraints
> = h-bonds. My question is: for the subsequent equilibration steps, I have read
> that one should use constraints = all-bonds, but I have also read that might
The constraint settings are not dependent upon the phase of the simulation;
these should be kept constant. For CHARMM, constraints = h-bonds.
> adversely affect 1-4 interactions. And what about DispCorr: should I keep =
> none or one of the other options -- or does it matter?
I don't know that anyone has done a systematic comparison, but I doubt that it
matters in any significant way for normal MD. Dispersion correction is
necessary for some systems with CHARMM36 (e.g. lipid monolayers) but not with
bilayers. AFAIK no one has looked at this with DNA.
> Thank you in advance. If there is some other resource that gives all the
> FF-specific settings, I would love to know about it.
The force field derivation papers are the first port of call. The methods there
should be considered canon unless otherwise revised later.
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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