Hi Mark, I do not do any equilibration, I only do energy minimization as in the "GROMACS Tutorial for Solvation Study of Spider Toxin Peptide". Please let me know if I need to do equilibration and what is the difference between energy minimization and equilibration as this is not clear to me.
Here is an mdp file for a run that actually completed successfully: title =Graphene ;warnings =10 cpp =cpp ;define =-DPOSRES constraints =none integrator =md dt =0.002 ; ps nsteps =10000 nstcomm =100 nstxout =100 ;nstvout =1000 nstfout =0 nstlog =100 nstenergy =100 nstlist =100 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 freezes graphene lattice energygrps = Grph NH3 energygrp_excl = Grph Grph freezegrps = Grph ; Freeze graphene lattice freezedim = Y Y Y; in all directions Tcoupl =berendsen tau_t =0.5 0.5 tc-grps =NH3 Grph ref_t =300 300 ;coupl = parrinello-rahman ;tau_p = 1.5 ;compressibility = 1.3 ;ref_p = 0.061 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 And here is a copy of an mdp file for a run that did not complete successfully: title =Graphene ;warnings =10 cpp =cpp ;define =-DPOSRES constraints =none integrator =md dt =0.002 ; ps nsteps =30000 nstcomm =500 nstxout =500 ;nstvout =1000 nstfout =0 nstlog =500 nstenergy =500 nstlist =500 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 freezes graphene lattice energygrps = Grph NH3 energygrp_excl = Grph Grph freezegrps = Grph ; Freeze graphene lattice freezedim = Y Y Y; in all directions Tcoupl =berendsen tau_t =0.5 0.5 tc-grps =NH3 Grph ref_t =300 300 ;coupl = parrinello-rahman ;tau_p = 1.5 ;compressibility = 1.3 ;ref_p = 0.061 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Please let me know what you think might be the problem. Thanks Darrell >Date: Thu, 16 Jul 2009 09:47:49 +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: <4a5e6aa5.4040...@anu.edu.au> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >darre...@ece.ubc.ca wrote: >> Hi Mark, >> Yes, I know that the box dimensions are defined in the last line of the >> .gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm >> in the .gro file. > >OK. > >> I looked through my .gro file to ensure none of the atoms had coordinates >> outside the 38x38x38 box. While I was reviewing the file I did notice >> that some coordinates had negative values, slightly negative, but >> negative none the less. Could this be causing the segmentation fault >> between time step 10,000 and time step 30,000? Why wouldn't the >> negative coordinates cause a segmentation fault much earlier? > >The absolute value of the coordinates is irrelevant. > >Your choice of 2.0 for rcoulomb is likely suboptimal for PME. Some >smaller value is probably more efficient, but this will not be the cause >of your problem. > >What is your system preparation regime? (i.e. EM + equilibration) > >Can you post a corrected and current .mdp file? > >Mark > >>> Date: Wed, 15 Jul 2009 16:59:21 +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: <4a5d7e49.9020...@anu.edu.au> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> darre...@ece.ubc.ca wrote: >>>> 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. >>> The box dimensions are defined in the bottom line of the .gro file, and >>> not by the positions of the atoms in that file. If you haven't ever set >>> them to be suitable for your coordinates with editconf, then they might >>> not be. >>> >>> Mark >>> >>> 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 >>>> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> 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! >>> >>> End of gmx-users Digest, Vol 63, Issue 61 >>> ***************************************** >>> >> _______________________________________________ >> 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 >> > > _______________________________________________ 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
