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 <[EMAIL PROTECTED]>: > > 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 > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > 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. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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