[gmx-users] g_rdf again

Rama Gullapalli quantrum75 at yahoo.com
Wed Nov 1 15:21:44 CET 2006

Dear All
  I am running a simulation of a DPPC bilayer. I am trying to compute the  INTER molecular RDF s of the P-P atoms, N-P atoms and N-N atoms in the  head of the bilayer. I have 2 questions,
  1) When I compute RDF using g_rdf, instead of a getting a smoothly  decaying curve at close distances (<0.3 nm) I get a spike (at around  0.22 nm). Is this due to INTRAmolecular RDF contribution? 
  2) If so, I probably need to increase the nexcl using a new tpr file  right? What I am wondering is, how much do I need to set the nexcl for  a DPPC molecule and what is the basis for it?
  Thanks a lot
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