[gmx-users] Magic error xtc?

[Justin A. Lemkul]

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

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