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

From: David A Case <>
Date: Thu, 5 Apr 2012 10:33:37 -0400

On Thu, Apr 05, 2012, David A Case wrote:

> 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.

Update: the "similar" problems had to do with restart files, not with
trajectory files. So that experience may not be relevant here.


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Received on Thu Apr 05 2012 - 08:00:04 PDT
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