[gmx-users] Question about Coarse-grain martini option of mdp file
jalemkul at vt.edu
Sun Feb 12 22:51:12 CET 2017
On 2/12/17 4:45 PM, ali.khourshaei71 at student.sharif.edu wrote:
> Dear Gromacs users,
> I've searched the Internet and I found that in .mdp file for
> Coarse-grain modeling people don't use DispCorr = EnerPres and
> refcoord_scaling = com (http://cgmartini.nl/). But, these options are
> active in All-atom ( Justin's tutorial). why they do that?
Because the tutorial .mdp files should not be considered universal. Details
differ between force fields, particularly the nonbonded setup and use of
As for refcoord-scaling, that should be a generic setting that is applied during
restrained equilibration to determine the origin of the biasing potential. But
I'm not prepared to make any blanket statements about why a given file would or
would not use that option.
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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