[gmx-users] Gromacs vs. Ab initio charges

[David van der Spoel]

On Mon, 2003-05-05 at 08:59, quantix1 at gmx.de wrote:
> Hi Vojtech,
> 
> force field charges are usually taken from quantum calculations (normally ab
> initio).
> The electrostatic potential  on a grid of points around the molecule is
> calculated
> from the wavefunction. The atomic point charges are then fitted to represent
> the ESP
> as good as possible. There are several methods available to do that. Look
> for RESP 
> or CHELPG in the literature. So basically, the FF charges are ab initio
> charges, although
> you might know that the atomic charge is not a quantum machanical
> observable. This
> means there is no way to assign the electrons of the molecule to specific
> nuclei uniquely. 
> The charges based on a fit of the ESP just seem to work best with force
> fields.
> 
The problem with the GROMOS force field is that there is no recipe for
generating charge like in e.g. Amber. Evrything is handtuned, and e.g.
the charges in use today for protein backbone have been around for 20
years, not because they are perfect, but because noone dares to change
anything that works more or less.

So the "recommended" way for developing models compatible with GROMOS is
to use parameters from similar groups. An alternative to this is to use
the OPLS force field ofcourse. I think there are recipes there for
generating parameters.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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