[gmx-users] g_rdf -[no]com

[Vasilii Artyukhov]

Oh yes, the -rdf option! And the run input file! That makes me feel kinda
stupid... Thank you very much & sorry for the dumb questions.

But still, having read the help again, I don't quite get the logic behind
g_rdf -com -rdf atom -n -s giving me an all-zero output for the RDF between
the COM of the molecule and water oxygen (which is I suppose what I request
it to produce). However, using -rdf mol_com seems to work fine.

2008/1/11, David van der Spoel <spoel at xray.bmc.uu.se>:
>
> 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
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