[Molecularmechanics] first steps

[Konrad Hinsen]

On Tuesday 21 October 2003 15:31, David van der Spoel wrote:

> I wouldn't want to give up on XMLized force fields yet. The problems
> Konrad describes in Amber are due to an interweaving of code and data,
> i.e. part of the information is in the algorithm. It may be hard to
> disentangle those in a specific case like Amber, but this is exactly the
> reason why we started to think about this in Gromacs. We do have some

The same problem exists in CHARMM and as far as I can tell in GROMOS. It can 
of course be overcome by a redefinition of the force fields (which would 
still be physically equivalent of course). If we can get the developers of 
the main force fields to work on this, I am all for it. I just don't want to 
wait for this to happen before starting to work on a common structure 
representation, which would be useful in itself even without a unified force 
field description.

> which makes implementing other FFs a pain. As soon as you have the
> complete description of the force field in XML however, the largest
> problem is solved.

Sure, but I expect this to be quite difficult to achieve.

Konrad.
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