[gmx-users] RDF in a droplet

Alex alexanderwien2k at gmail.com
Thu Dec 13 19:28:13 CET 2018

Dear all,
I have a system contains dispersed molecules of A(# 29) and B(# 14) in
water. A droplet is formed by molecule of A and B after 100 ns of MD
simulations where the B is supposed to more or less be like a shell around
A as a core.
I want to know the relative positions of molecules of A and B (or at least
some atoms of them) respect to each other or respect to the center of mass
of the formed droplet if possible. I guess the GMX RDF can do the job, so,
I am using below command; would you please help me improve the rdf or
please let me know what is wrong with the commands

gmx rdf -f md.xtc -s md.tpe -n index.ndx -o rdfB.xvg -b 99000 -selrpos
mol_cog -ref A -sel B

gmx rdf -f md.xtc -s md.tpe -n index.ndx -o rdfA.xvg -b 99000 -selrpos
mol_cog -ref A -sel A

Thank you

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