Thanks so much, Chris. I will check wiki. -Xianghong Qi On Fri, Nov 7, 2008 at 10:44 AM, <[EMAIL PROTECTED]> 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 >> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Some people make the world more special just by being in it.
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