Re: [AMBER] Odd coordinate writing problem in pmemd.MPI

From: David A Case <>
Date: Thu, 5 Apr 2012 09:55:32 -0400

On Thu, Apr 05, 2012, wrote:
> I have just experienced a strange coordinate writing issue with a pmemd
> simulation. I ran a 1 ns standard NPT MD of a small solvated protein
> writing to disk very often (10 gig total traj size), when at a random
> point (after 418ps) the structure when viewed in vmd appears to become
> completely scrambled.

See the archives for discussion of what sound like similar problems. For lots
of reasons, I'd recommend using netcdf files instead of the old formatted
ones. That might solve problems like this one.


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Received on Thu Apr 05 2012 - 07:00:03 PDT
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