[gmx-users] COM RDF

Dr. Vitaly V. G. Chaban vvchaban at gmail.com
Wed Jul 4 19:07:17 CEST 2012

Dear GROMACS people -

I am calculating radial distribution function between the centers of
mass of two large particles in a periodic box.

My command is --  g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f conf.gro

My index file contains two groups of atoms standing for the first and
the second supraparticles whose centers-of-mass I am interested in.
Since here I provide the "conf.gro" file rather than a trajectory, I
expect to get just one peak in my RDF, but instead I get multiple
peaks at different separation distances (please, see
http://i47.tinypic.com/24m826v.jpg). The groups of atoms in the index
file are separated spatially, if this may matter.

Would anyone kindly explain how the COM RDF function works? My
ultimate purpose is to depict how the distance between those two
centers-of-mass evolves in time.

Thank you.

Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216

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