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 >
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