[gmx-users] how can we restrain ion position?
jalemkul at vt.edu
Sun Sep 14 13:57:07 CEST 2014
On 9/13/14 10:22 AM, Albert wrote:
> I am just wondering how can we restrain the ion positon? Shall we use genrestr
Is the ion diffuse in solution or bound to something else (protein, etc)?
Position restraints are always the same, you need to apply a
[position_restraints] directive within the appropriate [moleculetype]. genrestr
is overkill for restraining a single ion, just write the directive by hand. The
main issues are: (1) if the ion is just part of the solvent, then you have to
change ions.itp, which restrains ALL of the ions of that type and (2) if you
want to restrain one mobile ion, you have to create a totally separate
[moleculetype] for it.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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