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
Rama
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