[gmx-users] Problem with g_rdf

Justin Lemkul jalemkul at vt.edu
Tue Feb 19 21:17:28 CET 2013

On 2/19/13 3:10 PM, Thomas Schlesier wrote:
> Dear all,
> I have a question regarding g_rdf.
> My system consits of 10 disacchardids (in the following A-B, with
> A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF
> (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B
> A-A and B-B is no problem.
> But for A-B g_rdf determines the intermolecular contribution (which i want) AND
> the intramolekular contribution (which i wanted to be excluded).
> Any (nice) ideas to solve this problem for GMX 4.0.7?
> Long way would be to calculate each intermolecular contribution individual and
> average over all. Would require some scripting :( so any better solutions are
> welcome.

Create a topology with a value of nrexcl sufficient to exclude all 
intramolecular interactions and create a .tpr file from it.  Use that as input 
to g_rdf.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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