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

From: <>
Date: Thu, 5 Apr 2012 10:58:48 -0400 (EDT)


> 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


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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