I think I know the problem. I looked through gmx_dist and the distance is calculated using the center of mass of the group. Since I am using Vsite the mass of CB in ALA is set to zero. Is that correct?
Thanks, Ilya On Tue, Mar 9, 2010 at 11:44 AM, David van der Spoel <sp...@xray.bmc.uu.se>wrote: > On 2010-03-09 20.01, Joe Joe wrote: > >> I also just tried on a different ALA and got the same problem. >> > > can you please submit a bugzilla and upload files to reproduce the problem? > > >> Ilya >> >> >> On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe <ilcho...@gmail.com >> <mailto:ilcho...@gmail.com>> 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 <ilcho...@gmail.com >> <mailto:ilcho...@gmail.com>> 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 >> <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> 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 >> <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >> <mailto:sp...@xray.bmc.uu.se >> <mailto:sp...@xray.bmc.uu.se>>> 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. >> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >> <mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se >> >> >> >> >> http://folding.bmc.uu.se >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>> >> >> 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 >> gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> 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. >> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >> http://folding.bmc.uu.se >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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 >> gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> 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. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > 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/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/mailing_lists/users.php >
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