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,
Sarah
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