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."
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 > > -- 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