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

Kaihsu Tai kaihsu at biop.ox.ac.uk
Fri Oct 17 15:39:57 CEST 2003

Thank you for the response, David.  Is it possible for me to
get the code for your Python interface?  I could write some
drivers for our database (BioSimGrid) based on your code,
and send patches if necessary.  Cheers.

David van der Spoel, 2003-10-17 12:31:06+0200:
> 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
> access.
> I would like to suggest that we discuss these things further on the
> gromacs developers mailing list (please subscribe at:
> http://www.gromacs.org/mailman/listinfo/gmx-developers/)

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