Dear GMX Users,
Keyword: metal, energy minimization, segmentation fault I have pinpointed the source of EM error. EM succeeds only without potassiums. I used PDB 1r3j and changed the TL to K. You can download the my 1r3j here and reproduce the error like this. $gmx pdb2gmx -f 1r3j_kchannel.pdb -o 1r3j.gro -ignh -water tip3p $gmx grompp -f minim.mdp -c 1r3j.gro -p topol.top -o em.tpr $mpirun -np 20 gmx_mpi mdrun -ntomp 1 -s em.tpr Thanks for any solutions. ######################The minim.mdp file###################### define=-DPOSRES ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions ###################################END########################## ############################EM Error############################ Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 [gpu-new:22930] *** Process received signal *** [gpu-new:22930] Signal: Segmentation fault (11) [gpu-new:22930] Signal code: Address not mapped (1) [gpu-new:22930] Failing at address: 0xfffffffe01bf6dd0 [gpu-new:22930] [ 0] /lib64/libpthread.so.0[0x383660f710] [gpu-new:22930] [ 1] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6c36f)[0x2b1966ebe36f] [gpu-new:22930] [ 2] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6d65f)[0x2b1966ebf65f] [gpu-new:22930] [ 3] /home/duyu/software/gcc-4.9.4/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b196d7a58cf] [gpu-new:22930] [ 4] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_Z17nbnxn_put_on_gridP12nbnxn_searchiPA3_fiPfS3_iifPKiS2_iPiiP16nbnxn_atomdata_t+0xecd)[0x2b1966ec28fd] [gpu-new:22930] [ 5] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(dd_partition_system+0x2c67)[0x2b19661ed6b7] [gpu-new:22930] [ 6] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe0379d)[0x2b1966e5579d] [gpu-new:22930] [ 7] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx8do_steepEP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiP11gmx_vsite_tP10gmx_constriP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP9t_mdatomsP6t_nrnbP13gmx_wallcycleP9gmx_edsamP10t_forcereciiiP12gmx_membed_tffimP23gmx_walltime_accounting+0x353)[0x2b1966e69aa3] [gpu-new:22930] [ 8] gmx_mpi(_ZN3gmx8mdrunnerEP12gmx_hw_opt_tP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiPiiiffPKcfSE_SE_SE_SE_iliiiiiifffim+0x190a)[0x4101ca] [gpu-new:22930] [ 9] gmx_mpi(_Z9gmx_mdruniPPc+0x1766)[0x421516] [gpu-new:22930] [10] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x2a3)[0x2b19661a5693] [gpu-new:22930] [11] gmx_mpi(main+0x7c)[0x40cd3c] [gpu-new:22930] [12] /lib64/libc.so.6(__libc_start_main+0xfd)[0x383621ed1d] [gpu-new:22930] [13] gmx_mpi[0x40cb79] [gpu-new:22930] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 0 on node gpu-new exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- ###################################END########################## -- Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 -- 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.