[gmx-users] Question about Coarse-grain martini option of mdp file

[Justin Lemkul]

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 
dispersion correction.

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

-- 
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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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