VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed May 07 2008 - 15:21:47 CDT

hi everybody,

since the topic of how to run bigdcd in batch mode
and how to make it handle file types different from
dcd comes up every once in a while, i've tried to
find a way to incorporate this in a portable way.
i've also taken the liberty to replace the use of
some obsolescent APIs with recommended ones.

i would very much appreciate any feedback on the
attached version 2.0 of the script.

it should work 'as is' for all previous uses of the
unmodified bigdcd script. but there are two new options:

1) the second argument to the bigdcd procedure can be
either "auto" or any file type known to VMD (e.g. "dcd",
"trr", "xyz", "xtc" and so on). then the script will load
all files as the given type or try to guess from the file
name which type you have when using "auto".

2) in your calling script you can now call "bigdcd_wait"
and the script should wait until all frames are processed.

the very nature of how bigdcd works makes the latter somewhat
prone to race conditions, so it would be very helpful if
users of the older (hacked?) version(s) of the script could
verify that it is working in the expected way, particularly
for textmode trajectory files and on very slow or very fast
processors.

thanks,
    axel. 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
    Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.