If it is a netcdf problem, is it not possible to just have a quick script
that uses ptraj to convert from binary back to human readable?
On Thu, Apr 5, 2012 at 10:58 AM, <steinbrt.rci.rutgers.edu> wrote:
> 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.
>
> Hi, no my trajectory does not recover, the last 60% became garbage :-/ I'd
> say it is a writing problem, too, as the internal coordinates apparently
> stay fine, but nevertheless, this seems worrying to me... I restarted my
> runs with serial pmemd to check if it happens again.
>
> >> > of reasons, I'd recommend using netcdf files instead of the old
> >> formatted
>
> I know, but I like about the old style files that my simple perl scripts
> can parse them and I can just look at the numbers to check for errors like
> this.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 05 2012 - 08:30:04 PDT
