Yes.. I used VMD for conversion... On Sat, Apr 28, 2018 at 12:50 PM, RAHUL SURESH <drrahulsur...@gmail.com> wrote:
> Hi > > Sounds strange to my little knowledge. How I would justify is, it may be > due to the conversion from NAMD [dcd] to Gromacs profile [trr] though not > sure. > > So you have converted the file format using VMD? > > > > On Sat, Apr 28, 2018 at 12:26 PM, Sahithya S Iyer <sah2...@gmail.com> > wrote: > > > Hi, > > > > Thanks for the reply. I am only doing a rerun of a trajectory that has > > already evolved without any dynamic load balancing problems. > > -rerun only recalculates energies right. I don't understand why the same > > trajectory is giving decomposition error now. > > > > On Sat, Apr 28, 2018 at 12:11 PM, RAHUL SURESH <drrahulsur...@gmail.com> > > wrote: > > > > > Hi. > > > > > > That indicates a problem with dynamic load balancing. Try to build > > > different sizes of the box. > > > > > > On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer <sah2...@gmail.com> > > > wrote: > > > > > > > Hi, > > > > > > > > I am trying to calculate interaction between specific residues using > > gmx > > > > mdrun -rerun flag. The trajectory was in a dcd format, which I > > converted > > > to > > > > a trr file. I get the following error - > > > > > > > > Domain decomposition has not been implemented for box vectors that > have > > > > non-zero components in directions that do not use domain > decomposition: > > > > ncells > > > > = 1 8 1, box vector[2] = 0.000000 10.536000 0.000000 > > > > > > > > Can someone please tell me what could be going wrong here ? > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at http://www.gromacs.org/ > > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.