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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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