[gmx-users] Water-Zinc interactions
jalemkul at vt.edu
Mon Jun 2 20:26:41 CEST 2014
On 6/2/14, 2:13 PM, Steve Seibold wrote:
> I am doing a simulation of a protein with zinc ligands..When looking calculating the distance between the Zinc and the water, I am getting distances that go as low as 0.3-0.4 Angstroms. This seems too close to me..Is this close contact due to the errors in trajectories??
Distances this close should be totally obvious upon visual inspection. Does
visualization confirm that such close contacts are occurring? How are you
measuring the distances? If you're just using g_dist to measure the COM
differences between waters and Zn, then you're not showing anything useful, just
that the center of the box is more or less close to the center of the box :)
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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