[gmx-users] criticism invited...

[Christoph Freudenberger]

Paul Barrett wrote:
> My (alledged) solution: combine this hydrogen with its neighbouring
> oxygen by:
> 
> 1) make a new dummy atom in ffgmx.atp file to represent the OH group as
> a single atom with mass = sum of components.
> 2) modify ffgmx.rtp for ATP to remove the hydrogen and turn the Oxygen
> in to the OH blob with a charge = sum of components.
> 3) modify my pdb file to remove the hydrogen
> 
Well, what you just did is try to implement a united atom model
for the OH group.
I suppose this is one of the parts of ffgmx.rtp you changed:
  AO3PG    OA  -0.548    12
  AH3PG    HO   0.398    12

IMHO there are a couple of problems about your approach:
1. The OH is very polar (see above). If you add both charges,
the strong dipole of the group is lost, which will give you
a very bad representation of it's functionality.
2. The LJ parameters of the united OH-group should be
redefined.

I cannot judge how much this will effect the results in your special case,
but i don't think it's "good force field practice".

I would try to add the hydrogens mass into the oxygen
and define the hydrogen as a dummy keeping it's charge
and LJ's.

regards
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785