[gmx-users] peculiar water behavior
jalemkul at vt.edu
Wed Jun 18 13:42:15 CEST 2014
On 6/17/14, 5:20 PM, Chetan Mahajan wrote:
> Thanks, Justin. That makes it clear. I have one small question: I do not
> know how does position restraint algorithm work with other things in
> gromacs, but doesn't it generate a lot of stress due to slab moving from
> center to near box boundary despite of position restraints, when -com
> option is used for refcoord-scaling? If there is a lot of stress, would
> this stress affect simulation results?
You can get a sense of that by extracting the energy associated with the
restraints from the .edr file.
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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