[gmx-users] COM RDF

Dr. Vitaly V. G. Chaban vvchaban at gmail.com
Wed Jul 4 19:31:50 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.
> You also need to use the -com flag to use the COM of the reference group.
> -Justin

The -com flag changed the output (please, see
http://i48.tinypic.com/29uuo7b.jpg) but there is still a number of
embarassing peaks after 7nm. Given the positions of these
supraparticles, I would expect maximum about 10nm whereas the box side
is 26nm.

>From the g_rdf help message --

The option -rdf sets the type of RDF to be computed. Default is for atoms or
particles, but one can also select center of mass or geometry of molecules or
residues. In all cases, only the atoms in the index groups are taken into

I understand this in the following way. The centers-of-mass of the
groups in the index file are computed and further the calculation
proceeds as if these COMs were regular atoms. If I have only two
groups, I should get one maximum.

Am I not correct?


More information about the gromacs.org_gmx-users mailing list