[gmx-users] Regarding Random expulsion molecular dynamics in Gromacs for ligand exit study
jalemkul at vt.edu
Mon Apr 11 12:27:33 CEST 2016
On 4/11/16 2:55 AM, meenakshi wrote:
> Dear All,
> I am interested in studying ligand exit using Random Expulsion molecular
> dynamics technique. I went through mailing lists and internet search but could
> not find any links explaining implementation of Random expulsion technique in
> Although there is a paper on 'Molecular dynamics simulation of ligand
> dissociation from Liver fatty acid binding protein'. PLoS One. 2009; 4(6):
> e6081, which has implemented REMD technique in Gromacs but the procedure of
> Random expulsion molecular dynamics in Gromacs is not explained.
> Any help with the protocol in Gromacs would be greatly appreciated.
Questions about the methods of a published study should be directed to the
corresponding author(s) of that study. A quick look suggests that they might
have been utilizing either the pull code or acceleration options, and either
controlling the workflow with external scripts or modified code. The specifics
are up to the authors to explain to you.
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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