Dear GROMACS Gurus, I am experiencing a segmentation fault when mdrun executes. My simulation has a graphene lattice with an array (layer) of ammonia molecules above it. The box is three times the width of the graphene lattice, three times the length of the graphene lattice, and three times the height between the graphene lattice and the ammonia molecules. I am including the mdp file and the error message.
*************************************************************************** .mdp file title =FWS ;warnings =10 cpp =cpp ;define =-DPOSRES ;constraints =all-bonds integrator =md dt =0.002 ; ps nsteps =100000 nstcomm =1000 nstxout =1000 ;nstvout =1000 nstfout =0 nstlog =1000 nstenergy =1000 nstlist =1000 ns_type =grid rlist =2.0 coulombtype =PME rcoulomb =2.0 vdwtype =cut-off rvdw =5.0 fourierspacing =0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e-5 optimize_fft =yes ; This section added in to freeze hydrogen atoms at edge of graphene lattice to prevent movement of lattice ;energygrp_excl = Edge Edge Edge Grph Grph Grph freezegrps = Edge Grph ; Hydrogen atoms in graphene lattice are associated with the residue Edge freezedim = Y Y Y Y Y Y; Freeze hydrogen atoms in all directions ;Tcoupl =berendsen ;tau_t =0.1 0.1 ;tc-grps =protein non-protein ;ref_t = 300 300 ;Pcoupl = parrinello-rahman ;tau_p = 0.5 ;compressibility = 4.5e-5 ;ref_p = 1.0 ;gen_vel = yes ;gen_temp = 300.0 ;gen_seed = 173529 *************************************************************************** *************************************************************************** ERROR IN OUTPUT FILE [node16:25758] *** Process received signal *** [node16:25758] Signal: Segmentation fault (11) [node16:25758] Signal code: Address not mapped (1) [node16:25758] Failing at address: 0xfffffffe1233e230 [node16:25758] [ 0] /lib64/libpthread.so.0 [0x3834a0de80] [node16:25758] [ 1] /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6) [0x2ba295dd0606] [node16:25758] [ 2] /usr/lib64/libmd_mpi.so.4(do_pme+0x808) [0x2ba295dd4058] [node16:25758] [ 3] /usr/lib64/libmd_mpi.so.4(force+0x8de) [0x2ba295dba5be] [node16:25758] [ 4] /usr/lib64/libmd_mpi.so.4(do_force+0x5ef) [0x2ba295ddeaff] [node16:25758] [ 5] mdrun_mpi(do_md+0xe23) [0x411193] [node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40) [0x4142f0] [node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9] [node16:25758] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3833e1d8b4] [node16:25758] [ 9] mdrun_mpi [0x40429a] [node16:25758] *** End of error message *** mpirun noticed that job rank 7 with PID 25758 on node node16 exited on signal 11 (Segmentation fault). 7 processes killed (possibly by Open MPI) *************************************************************************** Could you please let me know what you think may be causing the fault? Much thanks in advance. Darrell Koskinen _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
