[gmx-users] Regarding Random expulsion molecular dynamics in Gromacs for ligand exit study

Justin Lemkul 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
> Gromacs.
> 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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