On 7/4/12 1:07 PM, Dr. Vitaly V. G. Chaban wrote:
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.
You also need to use the -com flag to use the COM of the reference group.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
