[gmx-users] Re: .xtc file is incomplete
xianghong001 at gmail.com
Fri Nov 7 19:10:25 CET 2008
Thanks so much, Chris. I will check wiki.
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.
> 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
>> 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 :)
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Some people make the world more special just by being in it.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users