Dear Alexey Zeifman, >From my experience it is just the nodes have to break down into some sort of >even multiple by dividing the domain decomposition size or vise versi. I >think somone elses answere was just to try it with a couple sizes for the >decomposition, as multiples of the number of nodes.
also your PME reserved nodes are probably too much or your wasting space, but I am not sure if this effects the domain decomposition or if all 20 nodes are thrown into that? Stephan Watkins -------- Original-Nachricht -------- > Datum: Tue, 14 Feb 2012 18:01:24 +0400 > Von: Alexey Zeifman <az...@mail.ru> > An: gmx-users@gromacs.org > Betreff: [gmx-users] Domain decomposition in FEP > Dear all, > > I'm trying to run FEP calculation of the ligand in the protein in water. > Performing NVT-dynamics for Lennard-Johnes perturbation using soft core > results in the following error: > > There is no domain decomposition for 20 nodes... > > I've checked out the log-file and found this: > > >Initial maximum inter charge-group distances: > > two-body bonded interactions: 1.474 nm, Bond, atoms 4371 4391 > > multi-body bonded interactions: 0.522 nm, Ryckaert-Bell., atoms 3747 > 3756 > >Minimum cell size due to bonded interactions: 1.621 nm > >Guess for relative PME load: 0.29 > >Will use 20 particle-particle and 12 PME only nodes > >This is a guess, check the performance at the end of the log file > >Using 12 separate PME nodes > >Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 > >Optimizing the DD grid for 20 cells with a minimum initial size of 2.026 > nm > >The maximum allowed number of cells is: X 3 Y 3 Z 3 > > > ->------------------------------------------------------ > >Program mdrun_mpi, VERSION 4.5.1 > >Source code file: domdec.c, line: 6428 > > >Fatal error: > >There is no domain decomposition for 20 nodes that is compatible with the > given box and a minimum cell size of 2.02621 nm > >Change the number of nodes or mdrun option -rdd or -dds > >Look in the log file for details on the domain decomposition > >For more information and tips for troubleshooting, please check the > GROMACS > >website at http://www.gromacs.org/Documentation/Errors > ->------------------------------------------------------> > > I understand that distance of 1.474 nm is rather big for bond! BUT I can't > find such a distance between atoms 4371 4391. The fragment of gro-file for > such index interval looks like this: > > 640LIG C4 4371 2.897 3.416 3.072 > 640LIG N3 4372 3.296 3.109 3.434 > 640LIG N6 4373 3.416 2.999 3.595 > 640LIG C6 4374 2.696 2.762 3.601 > 640LIG C7 4375 3.025 3.232 3.150 > 640LIG C8 4376 3.208 3.142 3.338 > 640LIG C9 4377 2.758 2.644 3.649 > 640LIG C10 4378 2.767 2.884 3.595 > 640LIG N4 4379 3.319 2.826 3.731 > 640LIG C11 4380 2.968 2.768 3.677 > 640LIG C12 4381 2.894 2.648 3.686 > 640LIG C13 4382 2.901 2.887 3.638 > 640LIG N5 4383 3.100 2.766 3.707 > 640LIG C14 4384 3.420 2.908 3.693 > 640LIG O1 4385 3.018 3.627 3.068 > 640LIG C15 4386 3.028 3.095 3.182 > 640LIG C16 4387 3.123 3.049 3.275 > 640LIG O2 4388 2.566 2.759 3.559 > 640LIG O3 4389 2.699 2.993 3.545 > 640LIG O4 4390 2.680 2.530 3.655 > 640LIG C17 4391 2.791 3.426 3.184 > 640LIG C18 4392 2.834 3.453 2.937 > > and the actual distance is 1.55 A - quite OK for single C-C bond. > > And another interesting fact is that it doesn't occur during FEP > calculation of the same system without soft-core and aimed at only charge > perturbation. > > I will appreciate any help regarding this. > > Alexey Zeifman > -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://www.gmx.net/de/go/freephone/ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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