[gmx-developers] Hardcoded (bad) parameters in dummy code...

Anton Feenstra feenstra at chem.vu.nl
Tue Jun 11 09:55:47 CEST 2002

Erik Lindahl wrote:
> Sorry if I sounded too hard - I was just quite tired after fixing a lot
> of undocumented and non-standard stuff in the OPLS parameters and
> articles, so I didn't get too happy when I found similar stuff in our
> own code :-)

I know the feeling ;-) and you're right: it shouldn't have been 
written that way. But sometimes you want to have it running and
you'll fix it afterwards, you think, but then 'afterwards' is not
a limited interval...

> OK - The initial position of the MCH3/MNH3 dummy masses are calculated
> from the input coordinates, but since there are constrainttypes defined
> for them it won't matter. Good - this means that it doesn't depend on
> any coordinates, apart from the dummy aromatics parameters....

That's the way I intended it, so that's good.

> I won't disable anything in the stable branch, but it must be fixed
> since the current setup is dangerous. One way could be to introduce a
> trivial database with entries for each NH3/CH3 group and the next heave
> atomtype and say which dummy mass should be used, or if it's planar.

Sounds good.

> I'm not sure what to do about the aromatics; TRP and HIS are quite a bit
> more complicated in most other forcefields since not all bonds are equal
> in the 5-rings. One alternative might be to replace the current
> hardcoded parameters with experimental values of indole & isoxazole ring
> geometry. That should be an improvement for G96 and Gromacs forcefields
> too...

It's not impossible to do it from the proper ff parameter values
(equilibrium bond lengths and angles). One of the major problems
is that all angles and bond lengths need not be compatible, in the
sense that all can be in the minimum simultaneously, so starting
the calculation of the dummy parameters from such an 'incompatible'
geometry will be unpredictable...

> In the development tree I think we should replace it completely
> (otherwise we don't have any incitament to fix it) and start writing a
> dummy database.

A solid kick in the @rse to get us going, then... ;-)

> An alternative might be to move all the automatic dummy stuff to
> grompp/mdrun to hide it from the topology...

Also a pretty good idea, since it has in principle nothing to do
with the topology itself (or with building blocks and the like).
Also, part (about half) of it is in grompp anyway, since only
there the ff parameters are available...


 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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