According to the suggestion I added the box to the trajectory using -box option of trjconv, using the following commands:
trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc then using the g_hbond on the output trjectory (traj_box.xtc) run successfully but gives the wrong number of H-bonds between the proteins atoms. I have also tried to process the output trajectory (traj_box.xtc) with trjconv using -pbc mol -ur compact options before using g_hbond, but again I have got wrong number of H-bonds. Please help me to rectify the error. On Fri, Jul 19, 2013 at 11:19 AM, bipin singh <bipinel...@gmail.com> wrote: > Thanks a lot Prof. David. I will try this. > > > On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel < > sp...@xray.bmc.uu.se> wrote: > >> On 2013-07-19 06:26, bipin singh wrote: >> >>> Hello all, >>> >>> I was using g_hbond to calculate H-bonds for a trajectory made from >>> several >>> individual snapshots from MD simulation, but because this trajectory does >>> not have the coordinates/information for simulation box, g_hbond is >>> giving >>> the following error: >>> >>> Fatal error: >>> Your computational box has shrunk too much. >>> g_hbond_mpi can not handle this situation, sorry. >>> >>> >>> Please let me know, if there is any way to rectify this error. >>> >>> >>> you can add a box to your trajectory using trjconv. >> >> -- >> 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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > > > > -- > *----------------------- > Thanks and Regards, > Bipin Singh* > -- *----------------------- Thanks and Regards, Bipin Singh* -- 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