[gmx-users] rdf at contact

Faezeh Pousaneh fpoosaneh at gmail.com
Wed May 30 16:46:10 CEST 2018


I have a system of similar molecules, I would like to obtain the rdf at
contact (meaning, at surface of one particle).
What I try is; I make an index file containing only central atoms of all
molecules, then I run:

gmx rdf  -f  NPT.xtc  -s  NPT.tpr  -n  index.ndx -pbc   -ref 1 -sel 0   -b

ref 0 is a single atom
ref 1 is rest of atoms

Then, I find the rdf value at r=contact (radius of a molecule) from rdf.xvg
My problem is I get very different values  for different time intervals
(after equilibrium) . Why is that so?

I appreciate if sb can help.
Best regards

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