[gmx-developers] Re: Python interface connecting Gromacs and BioSimGrid

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 17 12:31:06 CEST 2003

On Fri, 2003-10-17 at 12:11, Kaihsu Tai wrote:
> Gentlemen -- Should I carry on alone with my Python parsers 
> etc.?  Or is there hope of collaboration?  Thank you.
> Kaihsu Tai, 2003-10-14 16:56:34+0100:
> > Seriously, I would really appreciate if someone could please
> > provide parsers for '.gro' and '.xtc' files in Python.  That
> > will speed up the BioSimGrid work greatly.
> > 
> > (By the way, I think my colleague Stuart Murdock talked with
> > David van der Spoel at Cecam.  Hope that bettered our mutual
> > understanding.)

The more the merrier! 

Yes I am working (slowly) on these things, together with Konrad
Piwowarczyk from Krakow. Things being worked on include:
- Python interface to the most important files in gromacs (.xtc, .edr,
trr, .gro). Others, like .g96 have already been implemented in
openbabel, although it wouldn't be a big problem to do so. 
- GUI using tkinter (or more fancy maybe) where the dialog boxes for all
the programs are *generated* from the program code. We then only have to
make one glueing python script
- if all that works we can interface with other programs like MMTK
- if all that works we can open up the gromacs libraries for python

I would like to suggest that we discuss these things further on the
gromacs developers mailing list (please subscribe at:

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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