Dear All, I am running simulations of BMP2 protein and graphite sheet using implicit solvent model (mdp file is pasted below). The graphite atoms are frozen in the simulation and BMP2 is free to translate. I got an error "Step 1786210: The domain decomposition grid has shifted too much in the Z-direction around cell 0 0 0" after 1749.7 ps of the simulation.
I then restarted the simulation without changing anything using the cpt file created from the previous (crashed) run and the simulation continues. It has run for over 60 ps now and is continuing to run. This is something we tried based on a previous email on gmxlist from David van der Spoel. We are using gromacs 4.5.5. Any idea what this error may be due to? We know that the system is not blowing up since it continues to run with the cpt file. Thanks, Sapna #### Start MDP file ############ dt = 0.001 ; time step nsteps = 5000000 ; number of steps ;nstcomm = 10 ; reset c.o.m. motion nstxout = 10 ; write coords nstvout = 10 ; write velocities nstlog = 10 ; print to logfile nstenergy = 10 ; print energies xtc_grps = System nstxtcout = 10 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method pbc = no rlist = 1.5 rcoulomb = 1.5 rvdw = 1.5 implicit-solvent = GBSA sa-algorithm = Ace-approximation gb_algorithm = OBC rgbradii = 1.5 gb-epsilon-solvent = 78.3 Tcoupl = V-rescale ref_t = 300.0 tc-grps = System tau_t = 0.5 gen_vel = yes ; generate init. vel gen_temp = 300 ; init. temp. gen_seed = 372340 ; random seed ;constraints = all-bonds ; constraining bonds with H ;constraint_algorithm = lincs refcoord-scaling = all comm_mode = ANGULAR freezegrps = Graphite freezedim = Y Y Y #### End MDP file ############ -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 -- 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.
