VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 07 2012 - 12:40:13 CDT

Hi,
  The trajectory plugin we developed for the DCD format is very
highly tuned, and the file format is relatively simple, so it
much faster to parse than the Gromacs TRR format. Even the old
DCD file format is much slower than the experimental .js file
format in recent versions of VMD. Most of the performance difference
here has to do with way the individual floating point values are
parsed (and potentially byte-swapped) by the TRR reader.
It is conceivable that we could make the TRR reader faster by
re-engineering the code somewhat. Another option would simply be
to convert your TRR file to a .js file, and get a huge resulting
performance gain for all of your subsequent analysis and visualization
work. Going forward, I am putting much of my effort into making
VMD take full advantage of the more modern file formats like the
new .js format, which are always going to perform at least
2x to 4x faster than the old formats like DCD, TRR, etc. If
enough Gromacs users would like to see the TRR reader improved,
I can add it to the TODO list, but it'll never be as fast as
the new JS format, so conversion may ultimately still be a
better solution at some point.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 07, 2012 at 10:00:19AM -0700, patrick wintrode wrote:
> I've been using VMD to analyze the output of some Gromacs simulations and
> I've found that when I read in a .gro file and then load a .trr
> trajectory, the loading is *extremely* slow compared to .psf .dcd files.
>
> Is there some way to improve this or does VMD just not play well with .trr
> files?
>
> Thanks.
>
> Patrick L. Wintrode
> Department of Pharmaceutical Sciences
> University of Maryland 

-- 
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