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