[gmx-users] node decomposition' problem
I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error message: There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 6.47943 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition I read about in gromacs forums and I can force the thing's running with the option nt 1 (one node...). My problem is that I still want to run in parallel. Is it still that possible for my system or I'm doomed to the 1 core simulation -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Re: [gmx-users] node decomposition' problem
On 7/9/12 4:23 PM, Thales Kronenberger wrote: I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error message: There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 6.47943 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition I read about in gromacs forums and I can force the thing's running with the option nt 1 (one node...). My problem is that I still want to run in parallel. Is it still that possible for my system or I'm doomed to the 1 core simulation The minimum charge group size depends on a whole host of factors: http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm The large size you have obtained indicates there are likely problems with the .mdp file, topology, or both. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Re: [gmx-users] node decomposition' problem
On 7/9/12 4:25 PM, Justin A. Lemkul wrote: On 7/9/12 4:23 PM, Thales Kronenberger wrote: I'm trying to run a kinase (what means that I had ATP - large charged group) energy minimization and then MD. But when I put my protein together with its ligands I gotcha the follow error message: There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 6.47943 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition I read about in gromacs forums and I can force the thing's running with the option nt 1 (one node...). My problem is that I still want to run in parallel. Is it still that possible for my system or I'm doomed to the 1 core simulation The minimum charge group size depends on a whole host of factors: *Edit* minimum domain decomposition cell - I don't know where charge group came from... http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm The large size you have obtained indicates there are likely problems with the .mdp file, topology, or both. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
