I am looking the the gmxdump output and everything seems consistent. The only difference is that the numbering in the index file starts at 1 whereas in the gmxdump the arrays are indexed starting at 0. The coordinates look just fine.
Thanks, Ilya On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe <[email protected]> wrote: > I trjconv/ed xtc to pdb and loaded into vmd. The coordinates looked fine. > > I also > > tpbconv/ed topol.tpr to topol_subset.tpr. > > then I > > editconf/ed topol_subset.tpr to gro and looked at the coordinates. Index > file matched and structure looked whole in vmd. > > I will try the gmxdump > > Thanks, > > Ilya > > > > > On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel <[email protected] > > wrote: > >> On 2010-03-09 19.16, Joe Joe wrote: >> >>> yep. >>> >> Have you gmxdump/ed the xtc to check the coordinates are right? >> >>> >>> On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel >>> <[email protected] <mailto:[email protected]>> wrote: >>> >>> On 2010-03-09 19.09, Joe Joe wrote: >>> >>> Hi I am trying to post process and xtc trajectory using g_dist. I >>> am >>> trying to calculate the CA-CB distance of an Alanine residue but >>> I get >>> NAN in all the distance columns. It works for the other residues >>> I've >>> tried (i.e. SER, VAL). I am using vsites in my simulation and I >>> think it >>> may have some thing to do with the way gromacs outputs the CB >>> positions >>> in the xtc file when the CB is part of the vsite network. Any >>> thoughs? >>> >>> Thanks, >>> >>> Ilya >>> >>> Are you sure your index file matches the xtc/tpr? >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell & Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> [email protected] <mailto:[email protected]> >>> >>> http://folding.bmc.uu.se >>> -- >>> gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> >>> http://lists.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] >>> <mailto:[email protected]>. >>> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> [email protected] http://folding.bmc.uu.se >> -- >> gmx-users mailing list [email protected] >> http://lists.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 >> > >
-- gmx-users mailing list [email protected] http://lists.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
