Dear Gromacs users, I am trying to simulate a large system (roughly 3M atoms including solvent) on Gromacs version 4.5.5. I am having difficulty having mdrun execute parallel calculations. I have run several variations (described below) of attempting steepest descent minimization and the simulation finishes successfully only if I set the number of threads to just 1.
variation 1: mdrun -v -deffnm steep_to_1000 Result: Making 1D domain decomposition grid 8 x 1 x 1, home cell index 0 0 0 Program mdrun, VERSION 4.5.5 Source code file: /share/apps/pkg/gromacs-4.5.5/src/mdlib/domdec_top.c, line: 356 Fatal error: 8346 of the 4590648 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck variation 2: mdrun -v -deffnm steep_to_1000 -noddcheck Result: identical to variation 1 (6528 of the 4422192 bonded interactions ...) variation 3: mdrun -v -deffnm steep_to_1000 -nt 1 Result: Successfully finishes run without incident (but very slowly) I also tested a simulation of a smaller system (~15k atoms), which ran without incident on a 1D domain decomposition grid 8 x 1 x 1. What parameters do you recommend I change to allow for multithreading? Thank you in advance, Rachel Baarda -- 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.