[gmx-users] rdf at contact
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.
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