I also just tried on a different ALA and got the same problem. Ilya
On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe <[email protected]> wrote: > 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 >>> >> >> >
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