Sorry for my silly mistake. I have a doubt regarding the expected difference in total No. of H-bonds calculated with whole a MD trajectory (protein+solvent box) and H-bonds calculated with concatenated frames (only protein) from a MD trajectory.
I mean, will the number of H-bonds present at a particular time in a MD trajectory (protein+solvent), should be exactly same as number of H-bonds calculated using trajectory made of concatenated frames (only protein) from (if we look at number of H-bonds present at same point of time in both). Because I am not getting the exact match between the two, there is random difference of 1-3 H-bonds at some point of time. On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/19/13 4:17 AM, bipin singh wrote: > >> 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. >> >> > A 0.9-nm cubic box is likely too small to correctly accommodate even an > amino acid, let alone an entire protein. > > -Justin > > >> 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> >>>> <htt**p://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<h**ttp://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> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >>> >>> >>> -- >>> *----------------------- >>> Thanks and Regards, >>> Bipin Singh* >>> >>> >> >> >> > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > > -- > 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* -- 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