Thanks for Mark's prompt reply. I find there indeed are overlapping potassiums from each chain and I remove the extra potassiums then EM succeeds.
Yu > -----Original Messages----- > From: "Mark Abraham" <mark.j.abra...@gmail.com> > Sent Time: 2017-10-11 22:12:29 (Wednesday) > To: gmx-us...@gromacs.org, GMX-user > <gromacs.org_gmx-users@maillist.sys.kth.se> > Cc: > Subject: Re: [gmx-users] Fw: Potassium channel EM Segmentation fault > > Hi, > > This is probably a case of > http://www.gromacs.org/Documentation/Terminology/Blowing_Up and I suggest > you consider some of the investigation approaches documented there. > > Mark > > On Wed, Oct 11, 2017 at 4:07 PM Du, Yu <d...@sioc.ac.cn> wrote: > > > > > > > > > -----Original Messages----- > > From:"Du, Yu" <d...@sioc.ac.cn> > > Sent Time:2017-10-11 21:55:38 (Wednesday) > > To: GMX-user <gromacs.org_gmx-users@maillist.sys.kth.se> > > Cc: > > Subject: Potassium channel EM Segmentation fault > > > > 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 > > > > -- > > 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. > > > -- > 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. -- 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.