Thank you sir. The problem is sorted out. Decreasing number of processors did the trick. Thanks again
On Wed, 21 Aug 2019 at 22:02, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/21/19 12:30 PM, Dhrubajyoti Maji wrote: > > Many tanks Dr. Lemkul for your kind reply. I have checked the link. I > have > > done the equlibration step successfully but the error appears at > production > > run. The change is only that now I am writing the output trajectory. So, > if > > I had any problem in topology or mdp file then I think my equilibration > > should have been failed. I am a newbie and I can't understand what > exactly > > is going wrong. Any kind of suggestion will be highly appreciated. > > Use fewer processors. You can't arbitrarily split any system over a > given number of processors. Prior runs may have worked if, for instance, > box dimensions were different, but now you have to adjust. > > -Justin > > > Thanks and regards. > > Dhrubajyoti Maji > > > > > > On Wed, 21 Aug 2019 at 16:21, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> On 8/21/19 1:00 AM, Dhrubajyoti Maji wrote: > >>> Dear all, > >>> I am simulating a system consisting urea molecules. After > >> successfully > >>> generating tpr file while I am trying to run mdrun, the following error > >> is > >>> appearing. > >>> Fatal error: > >>> There is no domain decomposition for 72 ranks that is compatible with > the > >>> given box and a minimum cell size of 0.5924 nm > >>> Change the number of ranks or mdrun option -rcon or -dds or your LINCS > >>> settings. > >>> All bonds are constrained are by LINCS algorithm in my system and > >> dimension > >>> of my box is 3.40146 nm. I have checked gromacs site as well as mailing > >>> list but couldn't understand what to do. Please help me with the issue. > >> > >> > http://manual.gromacs.org/current/user-guide/run-time-errors.html#there-is-no-domain-decomposition-for-n-ranks-that-is-compatible-with-the-given-box-and-a-minimum-cell-size-of-x-nm > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> 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. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.
