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. 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. > -- 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.