[gmx-users] Calculating RDF Using Closet Atom

Boning Wu bw194 at scarletmail.rutgers.edu
Tue Aug 25 19:10:14 CEST 2015

Dear GMX Users,

Sorry to take your valuable time. I have a mixed liquid system simulated
using gromacs version 5.0.4, where I want to calculate radial distribution
between molecule type A and type B defining the distance between them by
either "center of mass of Molecule A" - " closet atom to Molecule A in
molecule B" or " closet atom to Molecule B in molecule A" - " closet atom
to Molecule A in molecule B" . Looks like it can be solved using gmx rdf
option " -surf", however I found in an earlier post that by Dr. Berk Hess
saying "g_rdf -surf mol counts the number of atoms within a distance r from
the surface,"

We tried something like
gmx rdf -f AB.xtc -s AB.tpr -o AB.xvg -surf mol -rdf mol_com << EOF
# 2 - molecules A, 3- molecules B

it gives an unnormalized curve as said in the manual. My question is, will
this command give what I want after normalization? If not, is there any
other option in gmx that can do what I want? What else package would you
suggest to use if this function is not available in gmx?

Thank you in advance,
Boning Wu
Graduate Student,
Rutgers University

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