[gmx-users] COM RDF

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 4 19:34:04 CEST 2012

On 7/4/12 1:31 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
> 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
> account.
> 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?

In theory, yes.  I have no idea how effective g_rdf is for this purpose.  From 
your initial description, if you're just trying to track COM distance over time, 
why not use g_dist?  That's precisely what it does.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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