[gmx-users] Magic error xtc?

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 22 19:36:30 CEST 2010

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.


> Thanks.
> N.P


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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