[gmx-users] How to recover the corrupted .xtc file?

[Myunggi Yi]

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.