[gmx-users] -com switch in g_rdf

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 24 00:03:42 CEST 2012

On 4/23/12 5:54 PM, Andrew DeYoung wrote:
> Hi,
> If you have time, I have a somewhat embarrassing question to ask.  It is
> embarrassing because I feel like I should be able to understand or search
> for the answer, but I have not had success.  So I apologize if this is a
> silly question (and it probably is).
> On the mailing list, I have read this post from several years ago:
> http://lists.gromacs.org/pipermail/gmx-users/2006-May/021743.html
> The poster asks if one can use the -com option in g_rdf to calculate the
> (benzene center-of-mass)-(benzene center-of-mass) radial distribution
> function.  Dr. van der Spoel responds and says that the -com option "only
> computes COM of the central group. What you want is not implemented."
> My question is, what is the "central group"?

The reference group.

> g_rdf asks the user to select two entries for computing the RDF.  Typically
> I have been doing atom-atom RDFs.  This is straightforward; if I have a
> system of water with atoms OW and HW, and I want to compute the OW-HW RDF, I
> just need to make two index file entries: one with all of the OW atoms, and
> one with all of the HW atoms.
> But what happens if I have a system of benzene and I want to compute the
> (benzene center-of-mass)-(benzene center-of-mass).  This is not possible in
> the current implementation, I guess, because the index file does not "know"
> about molecules (only about atoms).  My question is, what if I selected all
> of the atoms in my pure benzene system, and used this selection for both
> selections as prompted by g_rdf.  What would this compute if I used the -com
> switch?  Since the index file does not know about molecules, it wouldn't
> compute the center mass of each benzene molecule.  But my question is, of
> what would it compute the center of mass?

If you select a system of pure benzene as the reference group, presumably the 
COM calculation will simply deduce the COM of the system and give you an RDF 
relative to this fixed point.



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


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