VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Mon Apr 18 2005 - 12:47:01 CDT

On Mon, 18 Apr 2005, Bogdan Costescu wrote:

BC> On Mon, 18 Apr 2005, Mgr. Lubos Vrbka wrote:
BC>
BC> > is it possible to somehow read (gzip) compressed trajectories to vmd?
BC>
BC> Are you sure that you want to talk about trajectories ? Usually
BC> trajectories are binary files (f.e. DCD) that appear to gzip as
BC> more-or-less random data and can be compressed very poorly if at all.
BC> This means lost CPU time: for compression - once and for decompression
BC> each time you want to read that trajectory, without any disk space
BC> saving.

indeed, there is no point to compress .dcd and similar trajectories
that are already in (packed) binary format. but there are some other
codes that don't do it and it is not always useful to convert to
a different format. some (e.g. .pdb 'trajectories') may contain
additional information that you want to preserve, or you may need
to re-read the trajectory and don't want to keep two copies around.

BC> Having on-the-fly decompression for individual structures stored in
BC> text files is probably a nice feature to have, so if John's to-do list
BC> is too short, maybe he can add this :-)

i don't think it is worth the hassle. also i have not checked, how
the external reference to zlib would be resolved. not to speak of
how you'd port it to a platform like windows.
the LD_PRELOAD hack with zlibc works very well on most platforms
where you could add zlib support easily. it is transparent and you
do not even need to modify VMD. just that it _can_ be done,
does not mean, that is _has_ to be done.

regards,
        axel. 

-- 
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Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
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If you make something idiot-proof, the universe creates a better idiot.