Hi Mark, I added the energy group exclusions as indicated in your previous response but am still experiencing the same problem. I looked at the .log files and see that in one log file it tells me that my box is exploding. However, I do not have many molecules in my simulation and therefore do not think that it is possible that my box is exploding from pressure.
Maybe if I re-state my simulation it will help you in providing me direction on what might be causing the problem. My simulation consists of a graphene lattice with a layer of ammonia molecules above it. The box is very large and there is lots of empty space in the box. So I am a little confused as to how the box could be exploding. Thanks again in advance for your help. Darrell Koskinen >Date: Fri, 03 Jul 2009 11:41:45 +1000 >From: Mark Abraham <mark.abra...@anu.edu.au> >Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4a4d61d9.6080...@anu.edu.au> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >darre...@ece.ubc.ca wrote: >> 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. > >Probably your system is exploding when integration fails with excessive >forces. You should look at the bottom of stdout, stderr, *and* the .log >file to diagnose. The error message you give below is merely the >diagnostic trace from the MPI library, and it not useful for finding out >what GROMACS thinks the problem might be. Further advice below. > >> *************************************************************************** >> .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 > >See comments in 7.3.24 of manual. You need the energy group exclusions. > >Mark > >> 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