[gmx-users] Problem with g_rdf

Thomas Schlesier schlesi at uni-mainz.de
Tue Feb 19 21:10:56 CET 2013

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.


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