[gmx-users] RDF analysis with respect to center of mass of otein

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================