[gmx-users] charges

[Anton Feenstra]

John Kerrigan wrote:
> Never let it be said that you overstate the obvious!  Ha! Ha!  Of course,
> charges remain fixed in a molecular mechanics computation.  However, Corina
> brings up a good point in regard to the methods that are used to compute
> these "fixed" charges.  If you compare QM calculations of ESP charges of
> different conformers of small flexible molecules, you will notice some
> dramatic differences in the partial atomic charges depending upon the method
> used (chelp).  The chelpg method in gaussian was developed by Breneman, et
> al. to address this shortcoming.  The RESP method developed by Bayly and
> Kollman was developed to address the problem of buried charges in proteins.
> The GROMOS crew has opted to scale their charges to correlate with
> thermodynamic properties as I understand it (please correct me).  All of
> these are good methods for their respective applications.  Who knows, which
> is best?  There is no established, reliable method for determining partial
> atomic charge experimentally.  For the small molecules, we can use dipole
> moments computed with these methods for comparison with experimental values;
> however, this still does not confirm whether or not the distribution of
> charge is correct.

Right - I can second you on all points. And would like to add still some
other (obvious?) ones myself. Atomic charges are no measureable quantity,
so there is much freedom to choose between various charge distributions.
Indeed, in Gromos they are 'just' another set of adjustable parameters,
used to reproduce other experimental data (densities, dielectric properties
and whatnots). Anyone who can establish whether that is a better (or worse)
choice than having a well-described method for deriving charges consistent
with a certain forcefield (as in OPLS and Amber) would earn a lot of
gratitude from all over the molecular simulation field, I'd think!


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|