[gmx-users] Magic error xtc?

[nishap.patel at utoronto.ca]

I am trying using prev_md.cpt file. I checked and it looks okay, so  
hopefully it will work. If not I will try using .trr files.
Thanks



Quoting Tsjerk Wassenaar <tsjerkw at gmail.com>:

> 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
> --
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