[gmx-users] g_rdf -[no]com

[David van der Spoel]

Vasilii Artyukhov wrote:
> Hi everybody,
> 
> I'm dealing with aqueous solutions of some small molecules. Just to clarify:
> 
> 1) When I type g_rdf, is the -com option on by default? g_rdf -h makes 
> me suspect it is...
read again.

> 2) When I type g_rdf -nocom, what point of the molecule does the 
> resulting RDF correspond to?
it works between atoms unless you use one of the other options.

> 3) g_rdf -h says that the -com option makes it calculate the RDF w.r.t. 
> the COM of the 1st molecule. What about the other one, how is it treated?
> 
have you tried it out at all?

 From g_rdf -h:
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. For molecules and/or the center of mass 
option a run input file is required. Other weighting than COM or COG can 
currently only be achieved by providing a run input file with different 
masses. Option -com also works in conjunction with -rdf.

> Thanks in advance,
> Vasilii
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se