there is nothing wrong about the rdf, except for some noise that would disappear for a longer simulation. the fact that you have a region with rdf values below 1 is just a diagnosis for the excluded volume in your system (the protein is dry inside, so the volume occupied by the protein do not contribute to the hydration).
cheers Andre On Tue, Nov 20, 2012 at 5:12 PM, shch406 <shch...@bpci.kiev.ua> wrote: > >I've never had an issue with similar commands. Can you provide us with > your > >full g_rdf command line? Have you verified that the index group for the > >arginine residue is correct? Can you provide a link to an image of the > >resulting RDF? > > >-Justin > > My full g_rdf command line is as in my first post (except path and full > names of files): > > /opt/software/gromacs/gromacs-4.5.3-intel/bin/g_rdf -f MT7w-145.trr -s > MT7w-145.tpr -n rs.ndx -o MT7w-145.RD-r205tipCOG.xvg -bin 0.05 -pbc -rdf > res_cog > > Atom numbers of the group in index file rs.ndx was taken from initial > conformation MT7w.gro file (3rd column) for NHH-NHH atoms of side chain tip > of 205 Arg. > These were verified to be correct. > > RDF curve image inserted as rdf.bmp: > <http://gromacs.5086.n6.nabble.com/file/n5003142/rdf.bmp> > > Igor > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Strange-form-of-RDF-curve-tp5003001p5003142.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- _____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
