[gmx-users] Magic Number Error in XTC file (read 0, should be 1995)

Justin Lemkul jalemkul at vt.edu
Sun Aug 13 18:30:05 CEST 2017

On 8/13/17 12:25 PM, ZHANG Cheng wrote:
> Hi Justin,
> Thank you. But how can I know where it goes wrong, and how can I avoid that?

gmx check showed you.  Looks like frame 13 is garbage, therefore anything after 
that becomes inaccessible.

Corruptions usually occur because of filesystem glitches.  The only way to avoid 
them is to use a more reliable system.

> If the trajectory is corrupt, why this 40 ns MD can still be continued to longer MD?
> Why it is okay in the beginning, but becomes corrupt later?

Because mdrun doesn't do trajectory file-checking on the fly, only if it 
completely fails to write something.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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