[gmx-developers] tabulated potentials, options & input files

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 28 14:52:04 CEST 2004

On Thu, 2004-10-28 at 14:37, Pim Schravendijk wrote:
> > The medium term plan is to get rid of grompp all together. Part of its
> > function would be in pdb2gmx, part of it in mdrun. All simulation
> > information would be stored in one XML file, generated directly by
> > pdb2gmx. However it may be necessary to use other tools to edit the
> > files as well (think genbox, editconf, etc.)
> I hope such a change would not be problematic when using imported 
> topogolies (e.g. from GROMOS) where the use of pdb2gmx is skipped. 
> Since it is XML the file could be (simply?) edited separately, or 
> generated by an external script, should something like that be possible?

Yes, since it is pure ascii text that is possible. Even though grompp
will not be needed anymore we will have to have tools for reading .top
files for backwards compatibility (i.e. grompp in disguise).

By the way would then also get rid of the tpr file...
David van der Spoel, PhD, Assoc. 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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