Hi Justin, I was experiencing the problem before someone suggested using editconf so I do not think the problem is being caused by editconf. But anyway here is my editconf command. Let me know if you a source of error in this command line.
editconf -f graphene.gro -n index.ndx -o graphene_ec.gro I did not want to add in additional space between the solvent and the box as I saw no reason for doing so. And hence that is why I originally did not use editconf. My box dimensions are 38nm x 38nm x 38nm. I used cutoffs of 2 nm & 5 nm for my system so ensure the cutoff occured at a distance where the potentials were stabalized (not changing). I guess I could use shorter cutoffs such as 1.5 nm & 2 nm and this may decrease my computation time. I also thought that I needed to use larger cut-offs since I am dealing in the gas phase and there is greater ditance between the atoms in my simulation than in liquid-based simulations. In the .log files, I do not see any LINCS warnings or neighborlist errors. I ran gmxcheck on a .trr file and was presented with the following output: ********************************************* Checking file mdtraj.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 # Atoms 10482 Last frame 5 time 1.000 Item #frames Timestep (ps) Step 6 0.2 Time 6 0.2 Lambda 6 0.2 Coords 6 0.2 Velocities 6 0.2 Forces 0 Box 6 0.2 ********************************************* I ran two additional simulations with different values for nsteps and nstxxxx paramaters and have the following to report: When I run a simulation with the following parameters it completes successfully and I see, in the log file, the system output every 100 time steps. nsteps =10000 nstcomm =100 nstxout =100 nstfout =0 nstlog =100 nstenergy =100 nstlist =100 When I run a simulation with the following parameters it fails with a sementation fault and, in the log file, I do not see system output every 500 time steps. nsteps =30000 nstcomm =500 nstxout =500 nstfout =0 nstlog =500 nstenergy =500 nstlist =500 Please let me know what you think might be the problem. Thank you very much. Darrell >Date: Mon, 13 Jul 2009 15:37:15 -0400 >From: "Justin A. Lemkul" <jalem...@vt.edu> >Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4a5b8ceb.4020...@vt.edu> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >darre...@ece.ubc.ca wrote: >> Hi Mark, >> I used editconf on my .gro file with zero space between my solvent and >> the box and the resulting box had the exact same dimension as the >> initial box. I also performed a number of simulation runs with different > >If you're using editconf to define zero space, what's the point? I only ask >because it is a potential source of error if you think you're adding zero >space, >but something else might be going on. Maybe you can post your editconf command >line. > >What are your box dimensions? Are cut-off lengths of 2.0 and 5.0 nm >appropriate >for your system? How did you determine that these cut-off's should be used? > >> mdp parameters hoping this would provide me some indication of the cause >> of the fault but to no avail. I looked through the log files, error >> files, and output files and could not find any output to help me >> identify the source of my error. >> > >It is very odd that Gromacs isn't report anything at all. No LINCS warnings? >No neighborlist errors? These would be in the .log file. > >> Could you please let me know how I can look at my structure at each point >> as you indicate below as I do not see any files output that provide me >> to do so? I tried to look at the .trr file but when I try to load it >> into VMD, it causes an error. I am assuming this error is caused because >> the .trr file did not complete correctly due to the segmentation fault. >> Please advise. >> > >How early is the segmentation fault occurring? I have found it useful >sometimes >to set nstxout (or nstxtcout) = 1 to try to catch the first few frames if the >explosion is occurring early. In any case, gmxcheck will help determine how >many frames are present, as well as the integrity of the file (broken frames, >etc). > >-Justin > >> Thanks. >> >> Darrell >> >>> Date: Tue, 07 Jul 2009 09:19:42 +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: <4a52868e.6010...@anu.edu.au> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> darre...@ece.ubc.ca wrote: >>>> 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. >>> Sure, but if there's something malformed with your model physics or >>> starting configuration, then large forces can make anything explode. >>> >>> Look at your structures at each point and see where things start to go >>> wrong. Make sure you've used editconf on your starting structure to >>> provide the right box dimensions. >>> >>> Mark >>> >>>> 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 >> > >-- >======================================== > >Justin A. Lemkul >Ph.D. Candidate >ICTAS Doctoral Scholar >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >======================================== _______________________________________________ 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
