[gmx-users] RDF analysis with respect to center of mass of otein
jalemkul at vt.edu
Fri Sep 19 23:48:56 CEST 2014
On 9/19/14 5:39 PM, Carlos Navarro Retamal wrote:
> Not at all. I’m using the .xtc file that comes from the simulation.
> What do you mean with the nrexcl issue? Is there a way i can fix it?
The g_rdf help text describes issues related to nrexcl, but probably it's
unrelated. I suspect you're probably getting issues related to periodicity,
since the COM of a protein "broken" across a box is coincident with the box
center, where you also have solvent. Remove periodicity and/or center the
protein in the box and re-run g_rdf.
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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