[gmx-users] errors on restart

gianluca santarossa gianluca_santarossa at fastmail.fm
Thu May 18 14:07:04 CEST 2006


Dear gmx users,
sometimes my simulations crash, and I need to restart them using the command
$ tpbconv -f traj.trr -e ener.edr
Sometimes it runs, while sometimes it gives me an error.
This is part of the output of tpbconv:

trn version: GMX_trn_file (single precision)
Read frame     11: step   5000 time    5.000

Using frame of step 5000 time 5
Opened ener.edr as single precision energy file
Reading frame      8 time    4.000
Last frame read 8
WARNING: Incomplete frame: nr      9 time    4.000

-------------------------------------------------------
Program tpbconv, VERSION 3.3.1
Source code file: enxio.c, line: 401

Fatal error:
Could not find frame with time 5.000000 in 'ener.edr'
-------------------------------------------------------

The problem is that the system did not write the last terms in ener.edr, 
while it wrote the terms in traj.trr.
In my grompp.mdp file I specified the same frequencies for energy and 
trajectory log:
nstxout      = 500
nstvout      = 500
nstlog         = 500
nstenergy   = 500
nstxtcout   = 500

What can I do to overcome the problem?
Thanks,
Gianluca



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