[gmx-users] Water-Zinc interactions

Justin Lemkul 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


More information about the gromacs.org_gmx-users mailing list