Dear users, I have a corrupted .xtc file. I can read only part of the whole frame in VMD. When I gmx check the .edr file, there is no problem with 5001 frames. However if I do gmx check the .xtc file, then I get only 2954 frames out of 50001 frames.
I used Gromacs 2019.6 with CUDA on a single node. I saved only xtc, edr, gro, cpt and log files. In addition, I cannot SCP the file to another machine. By a bash script (with PBS pro), I have run the simulation until md1.part0020.xtc without any problem. Is there a way to recover the xtc file? The following is the output from gmx check. GROMACS: gmx check, version 2019.6 Executable: /data/cluster/apps/gromacs/2019.6/bin/gmx Data prefix: /data/cluster/apps/gromacs/2019.6 Working dir: /data/........../trj Command line: gmx check -f md1.part0003.xtc Checking file md1.part0003.xtc Reading frame 0 time 110060.000 # Atoms 35936 Precision 0.001 (nm) Reading frame 2000 time 130060.000 WARNING: Incomplete frame: nr 2954 time 139600 Item #frames Timestep (ps) Step 2954 10 Time 2954 10 Lambda 0 Coords 2954 10 Velocities 0 Forces 0 Box 2954 10 ########################## edr file Command line: gmx check -e md1.part0003.edr Checking energy file md1.part0003.edr Opened md1.part0003.edr as single precision energy file frame: 55030000 (index 0), t: 110060.000 Last energy frame read 5000 time 160060.000 Found 5001 frames with a timestep of 10 ps. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
