Thanks Justin, It never happens to my simulations before, is there anyway to figure out what caused this corruption? the log file and screen outputs didn't mentioned any error message. I am wandering if it was caused by the unstable super-cluster I am currently using, because on another super-clusters, it never happened before.
On Wed, Apr 3, 2013 at 7:45 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/3/13 8:42 PM, mu xiaojia wrote: > >> Sorry for the typo, the last evidence"4) I also compared the generated >> files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching >> 100ns, the size would **NOT*** be the same as A." >> >> > You probably have a corrupted frame. The simulation continued and the > .trr file continued being written, so you see comparable file sizes. > > -Justin > > >> On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia <muxiaojia2...@gmail.com> >> wrote: >> >> Dear GMX users, >>> >>> I am not sure if someone has similar problems before. I cannot read half >>> of the frames from trr file after md simulation, and I believe my >>> simulation has already completed. >>> >>> I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the >>> only difference between A and B is they are npt simulations under >>> different >>> temperature (in mdp file, "ref_t" part )and such difference would not >>> cause >>> crash of the simulation. I have successfully finished A, everything looks >>> perfect (frames can be successfully extracted), but for B, I could not >>> extract last 70ns' frames from trr. >>> >>> 1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I >>> am using super computer so the job will be restarted for multiple times. >>> >>> 2) both simulation are 100ns, both log files indicate that they have >>> finished 100ns simulations. I checked my screen out put for B, whenever >>> it >>> restarted, the output on screen is correct and continuously ( something >>> like: 100000000 steps, 100000.0 ps (continuing from step 95963500, >>> 95963.5 >>> ps). >>> >>> 3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which >>> means only the first two restart simulation were recorded into trr, which >>> log files are not saying in this way.) >>> * >>> * >>> *For system A (the successful one), it shows* >>> >>> Reading frame 0 time 0.000 >>> # Atoms 72166 >>> Last frame 2000 time 100000.000 >>> >>> >>> Item #frames Timestep (ps) >>> Step 2001 50 >>> Time 2001 50 >>> Lambda 2001 50 >>> Coords 2001 50 >>> Velocities 2001 50 >>> Forces 0 >>> Box 2001 50 >>> >>> *for system B (the failed one)* >>> >>> Reading frame 0 time 0.000 >>> # Atoms 72166 >>> Reading frame 500 time 25000.000 >>> >>> >>> Item #frames Timestep (ps) >>> Step 596 50 >>> Time 596 50 >>> Lambda 596 50 >>> Coords 596 50 >>> Velocities 596 50 >>> Forces 0 >>> Box 596 50 >>> >>> 4) I also compared the generated files' sizes, A = B in trr, edr , gro, >>> cpt, if B crashes before reaching 100ns, the size would be the same as A. >>> >>> I am wondering what was wrong with my trr file of B . I appreciate for >>> any >>> suggestions! >>> >>> Sincerely >>> >>> Xiaojia >>> >>> >>> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
