VMD-L Mailing List

From: Bogdan Costescu (Bogdan.Costescu_at_IWR.Uni-Heidelberg.De)
Date: Mon Apr 18 2005 - 09:20:00 CDT

On Mon, 18 Apr 2005, Mgr. Lubos Vrbka wrote:

> is it possible to somehow read (gzip) compressed trajectories to vmd?

Are you sure that you want to talk about trajectories ? Usually
trajectories are binary files (f.e. DCD) that appear to gzip as
more-or-less random data and can be compressed very poorly if at all.
This means lost CPU time: for compression - once and for decompression
each time you want to read that trajectory, without any disk space
saving.

There are some text structure file formats that can contain several
structures and these can be used as a sort of trajectories; also,
CHARMM for example has the option of converting a binary trajectory
into a text one, with precision loss - these text files can be
compressed much better by gzip, but the text files are bigger than the
binary equivalents, so per-ensemble the gain is not worth it.

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

-- 
Bogdan Costescu
IWR - Interdisziplinaeres Zentrum fuer Wissenschaftliches Rechnen
Universitaet Heidelberg, INF 368, D-69120 Heidelberg, GERMANY
Telephone: +49 6221 54 8869, Telefax: +49 6221 54 8868
E-mail: Bogdan.Costescu_at_IWR.Uni-Heidelberg.De