[gmx-users] COM RDF

[Justin A. Lemkul]

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

-- 
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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

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