[gmx-developers] Shall we ditch gro and g96 files?

Erik Lindahl lindahl at cbr.su.se
Tue Apr 1 15:38:50 CEST 2008


On Apr 1, 2008, at 3:28 PM, Berk Hess wrote:
> I guess we would want two different formats.
> One for trajectories and one for simple configurtion files.
> David started this discussion with pdb, gro and g96, which are (at  
> least in Gromacs)
> mainly used for single configurations which are manipulated before  
> and after runs
> and not really used during runs.
> I think for this purpose we want a plain ascii format that is  
> somewhat flexible and extendible,
> but does necessarily need to be easily parallelizable or small.

Right. I guess one way could be to use XML for the simple one, but  
have an option to write a compact version (much fewer CR/LFs) such  
that each atom fits on a single line? XML-wise it would still be the  
same file, but then you could easily use grep/awk/perl/python for  
processing too?


Erik Lindahl   <lindahl at cbr.su.se>  Backup: <erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Center for Biomembrane Research, Dept. Biochemistry & Biophysics
Stockholm University, SE-106 91 Stockholm, Sweden
Tel: +46(0)8164675  Mobile: +46(0)704218767  Fax: mail a PDF instead

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