[gmx-users] Re: .xtc file is incomplete

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Nov 7 16:44:46 CET 2008

We have experienced this with NFS delay problems if you try to access  
the fie before it is completely written. On our most frustrating  
server, it can take up to an hour for the .xtc to be written in rare  
cases. For us, the biggest problem is when the .trr and .edr are  
completely written but the .xtc is not. Therefore one may not notice  
for many days and end up unable to make a nice movie to show your  
colleagues. To combat this, I developed an automated checkpointing  
script that you can find in the beginners->checkpointing jobs section  
of the gromacs wiki.


>     xianghong qi wrote:
>         Hello, everyone:
>         when I run simulation, I got incomplete .xtc file, incomplete
>         .trr file, but I have a complete log file. Then I use this
>         incomplete to create input file for mdrun, I got the reasonable
>         size of .tpr file.
>     I wouldn't trust that .tpr file to contain what you think it does
>     (size doesn't matter), at least in terms of the starting time.  It
>     will take the last frame as input, whatever it may be in the .trr file.
>         I am confused what happed there. Does anyone has some idea about
>         this?
>     Probably a hardware blip caused the last frame(s) to not be written.
>      I've had that happen before.
>         actually, when I rerun my simulation, I got the complete .xtc
>         file . I don't know why.
>     Probably because the blip didn't happen again :)
>     -Justin

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