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

[xianghong qi]

Thanks so much, Chris. I will check wiki.
-Xianghong Qi

On Fri, Nov 7, 2008 at 10:44 AM, <chris.neale at utoronto.ca> wrote:

> 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.
>
> Chris.
>
>
>     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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