Hi,<br>I'm checking my system and topology but I noticed a quite weird behaviour in<br>this concern.<br>When I run my simulation starting from a pre-optimized geometry, the simulation<br>crashes with segmentation fault.<br>On the other hand, when I run the same simulation but starting from the<br>geometry I generated "a priori" (without a first step of equilibration) the<br>simulation starts and ends correctly. The results look physically correct.<br>This is quite disappointing for me since I would expect problems when<br>pre-equilibration is missing and not when it is carried out as a preliminar step.<br>Furthermore, I find the same behaviour also for similar systems (different dimensions or shapes).<br>Maybe more experienced user found already the same behaviour or have an explanation.<br>Anyway, do you think that this could be due to some kind of error in the<br>topology/input or could my system be just quite critical to be modeled?<br><br>Thank you for your help.<br><br>Alb<br>
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----Messaggio originale----<br>Da: x.periole@rug.nl<br>Data: 19-ott-2009 2.04 PM<br>A: "albitauro@virgilio.it"<albitauro@virgilio.it>, "Discussion list for GROMACS users"<gmx-users@gromacs.org><br>Ogg: Re: [gmx-users] time steps and segmentation fault<br><br><br>The type of system you are simulating and the manner you prepared<br>are probably responsible for the crash ...<br>You should have a good look at it!<br><br><br>On Oct 19, 2009, at 3:29 PM, albitauro@virgilio.it wrote:<br><br>> Hi all,<br>><br>> I carried out a MD simulation using the MARTINI CG force field and I <br>> had some<br>> problems. The simulation stops immediately, reporting a <br>> segmentation fault:<br>><br>> **********************************************+<br>> Making 1D domain decomposition 2 x 1 x 1<br>> starting mdrun 'FIB'<br>> 200000 steps, 6000.0 ps.<br>> step 0<br>> [beta:06822] *** Process received signal ***<br>> [beta:06822] Signal: Segmentation fault (11)<br>> [beta:06822] Signal code: Address not mapped (1)<br>> [beta:06822] Failing at address: 0x34321d0<br>> [beta:06822] [ 0] /lib/libpthread.so.0 [0x7f7e49b38a80]<br>> [beta:06822] [ 1] mdrun_mpi [0x66549a]<br>> [beta:06822] *** End of error message ***<br>> mpirun noticed that job rank 0 with PID 6822 on node beta exited on <br>> signal 11 (Segmentation fault).<br>> 1 process killed (possibly by Open MPI)<br>> **************************************************<br>><br>> I have no WARNINGs in the output of the simulation.<br>> However, before, when running grommp I received 1 warning and 1 note:<br>><br>> ********************************************************<br>> WARNING 1 [file aminoacids.dat, line 1]:<br>> For proper thermostat integration tau_t (0.1) should be more than an<br>> order of magnitude larger than delta_t (0.03)<br>> ********************************************************<br>> and<br>> ********************************************************<br>> NOTE 1 [file ny6.mdp, line unknown]:<br>> The Berendsen thermostat does not generate the correct kinetic <br>> energy<br>> distribution. You might want to consider using the V-rescale <br>> thermostat.<br>> ********************************************************<br>><br>> I used a time step of 0.03 ps and a tau_t of 0.1 (suggested by the <br>> authors of MARTINI ff even when using a<br>> delta_t=0.04 ps). In any case, modifying the tau_t and avoiding the <br>> WARNING does not solve<br>> the problem.<br>><br>> The simulation starts and ends correctly if I use a delta_t=0.01 <br>> ps. However,<br>> this time step is not recommended for use with MARTINI ff because <br>> the range of<br>> time steps used for parametrization is 20-40 fs.<br>> Does anyone have any suggestion to solve the problem?<br>><br>> Many thanks,<br>><br>> AM<br>><br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before <br>> posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br><br><br>