Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups!
So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Many thanks! > > > On 7/31/13 10:49 AM, George Patargias wrote: >> Hello >> >> I am trying to calculate the RDF of water with water for a 10 ns MD of >> pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default >> -rdf option (atom). >> >> The problem is that the integration of the RDF curve up to the first >> minimum yields a zero value which is obviously not right >> >> Do you have any suggestions about this? Should I run g_rdf in a >> different >> way? >> > > Impossible to tell without seeing the RDF itself. If it doesn't look like > Figure 8.3 in the manual, then you've got a problem either with the > simulation > itself or the way the RDF was calculated. If it does, then you've got a > problem > with how you're integrating the curve. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > 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 > Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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
