[gmx-users] errors on restart

[Mark Abraham]

gianluca santarossa wrote:
> Dear gmx users,
> sometimes my simulations crash, and I need to restart them using the 
> command
> $ tpbconv -f traj.trr -e ener.edr

This shouldn't work, you need to give it a .tpr file too.

> 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

The .trr file has 11 frames up to time 5.000, if you read the manpage 
for tpbconv it will try to use the last .trr frame unless you tell it a 
different one.

> 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

The .edr file only had 8.something frames because it was interrupted 
while writing, and you need information from frame 11 because of the 
above default.

You can
a) prevent your simulations from crashing,
b) restart from the last frame common to both files, here 8, or
c) if they simulations are crashing in response to a signal, use a less 
vigorous one and gromacs will catch it and exit gracefully, writing output.

Mark