[gmx-users] -com switch in g_rdf

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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