[gmx-users] Closing of .trr and .edr files after running out of space

Sarah Witzke sawit02 at student.sdu.dk
Tue Feb 9 15:34:35 CET 2010

Dear gmx-users,

I have been very unfortunate (and stupid): I was running a simulation of 220 ns and due to limited space at our cluster-computer I was writing the .trr file and .edr file directly to another disc. That was un-clever since I did not write the .cpt file to that disc as well. As I am not the only one using the storage disc it ran out of space very shortly before the end of my simulation and I got this error message in the .log file:
  Epot (kJ/mol)        Coul-SR          LJ-SR        Coul-14          LJ-14
      DMPC-DMPC    2.60809e+02    2.19979e+02    3.95442e+02    7.50289e+01
       DMPC-SOL    6.74362e+02    2.11485e+02    0.00000e+00    0.00000e+00
        SOL-SOL    9.65717e+02    6.15314e+02    0.00000e+00    0.00000e+00

         T-DMPC          T-SOL
    2.81532e+00    1.30102e+00

Program mdrun_mpi, VERSION 4.0.4
Source code file: enxio.c, line: 212

File input/output error:
Cannot close energy file; it might be corrupt, or maybe you are out of quota?

I guess it is unable to close due to a lack of space? When running gmxcheck on the generated .trr file this message was printed:

Checking file dmpc.trr
trn version: GMX_trn_file (single precision)
Reading frame       0 time   10.000
# Atoms  35513
Reading frame    4000 time 40010.000
Program gmxcheck, VERSION 4.0.4
Source code file: trnio.c, line: 66

File input/output error:
Can not determine precision of trn file

This .trr file should be 220 ns and 18 G big, it is now 15 G.

Even though the .cpt file is only set to update every 15 min (default) there is only 3 min between state_previous.cpt and state.cpt. I think it is because it wrote a new .cpt just when finishing the run? But then non of the .cpt files are "old" enough to allow rerun from the point of the problem. Stupid of me.

Now, the simulations was supposed to be of 220 ns, but actually I only need around 150 ns for my purpose. So my question is whether there is anyy way to "close" the .trr file at the point it is at and then have a functional .trr file?

Best regards,

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