[gmx-users] Magic error xtc?

[nishap.patel at utoronto.ca]

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?




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
>
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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 the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php