Hi,
I've had the same thing happen, can't recall if I was using binary files or
not. I ended up just deleting those frames from the simulation. That is,
I assume also for your case that it goes back to being normal a few frames
afterwards (the longest stretch I had was 10 frames)? As you say, nothing
else about the simulation appeared perturbed, seemed like just a writing
problem.
~Aron
On Thu, Apr 5, 2012 at 10:33 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Apr 05, 2012, David A Case wrote:
>
> > On Thu, Apr 05, 2012, steinbrt.rci.rutgers.edu 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.
>
> ...dac
>
>
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Apr 05 2012 - 08:00:05 PDT
