[gmx-users] semi-permeable wall in gromacs

Justin Lemkul jalemkul at vt.edu
Thu Mar 10 15:58:23 CET 2016

On 3/10/16 4:44 AM, gozde ergin wrote:
> Dear Justin,
> Thanks for your respond, I assume there is a way to apply this restraint on specific molecules.
> Because my system is mixed with organic and water and I would like to apply these forces on organic molecules not water?

So apply flat-bottom restraints to whatever the organic molecules are.  It's not 
something specific to ions.  You set the restraints in the molecule's topology 
(in its [moleculetype]), construct a reference coordinate file that defines some 
unphysical coordinates to be used as the center of the restraint, and that's it. 
  I've described the process in detail before so check the archive.



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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