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

[Justin A. Lemkul]

xianghong qi wrote:
> haha, thanks for your explanation. Justin. So you think I should stop my 
> simulation.

If you are trying to re-run the first simulation, it may work just fine.  If you 
are using the .tpr file generated from the incomplete .trr, then it may work as 
well, just be careful that you know the actual starting time and configuration 
of your system.

-Justin

> I am trying to test whether my result is reasonable.
> Thanks anyway.
> -Xianghong Qi
> 
> 
> On Thu, Nov 6, 2008 at 3:03 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
>         Thanks.
>         -Xianghong Qi
> 
>         -- 
>         Some people make the world more special just by being in it.
> 
> 
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>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
> -- 
> Some people make the world more special just by being in it.

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================