[gmx-users] Отв: Position Restraint or remove COM from DNA
jalemkul at vt.edu
Tue Dec 2 02:31:38 CET 2014
On 12/1/14 4:13 PM, Hovakim Grabski wrote:
> I'm trying to find the binding sites of 6 Methylene Blue molecules on DNA.
> If I remove COM from the whole system, it also affects the Methylene Blue
> molecules, isn't it right?
You're not removing the motion of the molecules; you're removing artificial
drift of the system, e.g. net COM motion, that may accumulate. For solutes in
water, the only sensible choice is comm-grps = System.
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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