Hi, Clearly the conversion tool did not produce a file that conforms to the requirements GROMACS has for specifying periodic boxes. That may not work well even if you'd run mdrun without domain decomposition because the periodicity may not be understood correctly. Find out what was going on and how the conversion may have worked.
Mark On Sat, Apr 28, 2018, 09:54 Sahithya S Iyer <sah2...@gmail.com> wrote: > 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. > -- 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.
