[gmx-users] Magic error xtc?

[Tsjerk Wassenaar]

Hey,

Otherwise it's also still possible to do old style continuation with a
frame from the .trr/.edr file, provided you have those...

Cheers,

Tsjerk

On Thu, Apr 22, 2010 at 7:55 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> nishap.patel at utoronto.ca wrote:
>>
>> Hi Justin,
>>
>>    Well the way I continued my second part of the simulation was using my
>> md.cpt file. I checked my .cpt file and this is what I got:
>> Last frame         -1 time 83786.961 , so I guess my second run updated
>> the file, so does this mean I have to do the whole simulation again? or can
>> I use any of the other files for example .trr file? I thought it might be
>> that I don't have enough disk space?
>>
>
> Checkpoint files will over-write each other, but a backup is kept as
> (whatever)_prev.cpt; you may be able to use this file to re-start your run.
>  If md.cpt corresponds to a time where there is a viable frame in your
> trajectory, then there should be no problem re-starting it from this .cpt
> file.  That is, if the frame at (or after) 83790 is corrupt, re-starting
> from time 83786 should present no problem.
>
> Maybe you're out of disk space, but only you know if that's the problem :)
>
> -Justin
>
>>
>>
>>
>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>>
>>>
>>>
>>> nishap.patel at utoronto.ca wrote:
>>>>
>>>> Hello,
>>>>
>>>>   I am running simulations and I got Magic Number error: Fatal error:
>>>> Magic Number Error in XTC file (read 0, should be 1995)
>>>>
>>>>
>>>> Checking file md.part0002.xtc
>>>> Reading frame       0 time 48190.004
>>>> # Atoms  6533
>>>> Precision 0.001 (nm)
>>>> Reading frame  178000 time 83790.008
>>>>
>>>> Part one of the simulation ran fine, but it exceeded the run time  so I
>>>> ran it again, and got part0002.xtc file. Now it seems like my  part0002.xtc
>>>> file is corrupted, is there a way I can just run my  simulation again from
>>>> my first file without running the whole thing  again?
>>>>
>>>
>>> That's the nice part about checkpointing.  As long as you have the .cpt
>>> file from wherever you started the continuation, you can just re-run
>>> from that same point.  That's really what you did in the first place.
>>> If, for some reason, you've over-written or deleted that .cpt file,
>>> then you can only start from some later .cpt file, or in the worst
>>> case, all over again.
>>>
>>> -Justin
>>>
>>>> Thanks.
>>>>
>>>>
>>>> N.P
>>>>
>>>>
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
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>>
>>
>>
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands