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

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 28 14:33:27 CEST 2004

On Thu, 2004-10-28 at 14:23, Anton Feenstra wrote:
> Michael Brunsteiner wrote:
> > Is there a way to use tabulated potentials for 
> > intramolecular force field terms (bond-stretching, angle bending)
> > in gmx (3.2.1) ?
> Shouldn't be too hard to put in. But that is not why I answer.
> Thinking on this, I figured the way it now works is rather implicit,
> in that .mdp options and mdrun cmdline options are interdependent.
> Wouldn't it be better to have explicit table file name entries in the
> mdp file, and let grompp read the tables and include them in the tpr?
> That way, all ff info is *always* contained in the .tpr, in stead of
> being split. (The same would by the way go for the Pull and ED sampling
> stuff, I guess.) For the tabulated bonded interactions, it may even be
> sensible to include this in the .top/.itp files, which would probably
> necessitate some general table file parsing mechanism, and a general
> hookup into any type of interaction function...
> Any thoughts on this?

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.)

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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