Dear users, I have two questions.
1. I used to run typical simulations with the following command. gmx mdrun -deffnm md I had no problem. Now I am running a simulation with "Dry_Martini" FF with the following input. integrator = sd tinit = 0.0 dt = 0.040 nsteps = 1000000 nstlog = 5000 nstenergy = 5000 nstxout-compressed = 5000 compressed-x-precision = 100 cutoff-scheme = Verlet nstlist = 10 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 epsilon_r = 15 coulombtype = reaction-field rcoulomb = 1.1 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 tc-grps = system tau_t = 4.0 ref_t = 310 ; Pressure coupling: Pcoupl = no ; GENERATE VELOCITIES FOR STARTUP RUN: gen_vel = yes gen_temp = 310 gen_seed = 1521731368 If I use the same command to submit the job. I got the following error. I don't know why. ------------------------------------------------------- Program: gmx mdrun, version 2018.1 Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 224) Fatal error: When using GPUs, setting the number of OpenMP threads without specifying the number of ranks can lead to conflicting demands. Please specify the number of thread-MPI ranks as well (option -ntmpi). For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- So I did run simulation with the following command. gmx mdrun -deffnm md -ntmpi 1 Now the performance is extremely bad. Since yesterday, the log file still reporting the first step's energy. 2. This is the second question. Why? Can anyone help? Myunggi Yi -- 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.
