AMBER Archive (2008)

Subject: RE: AMBER: Electrostatic Energy Components

From: Ross Walker (
Date: Fri Nov 21 2008 - 16:33:30 CST

Hi Ilyas,

> Let's say that we have a C2H4 molecule. This molecule has max 3 bonds.
> Let's say that we do simulation in vacuum. What I would have thought was
> that because the force fields have bond/angle/dihedral terms to simplify
> the calculations, all the 1-2,1-3,1-4 interactions in a system will only
> depend on the the parameters defined for bond/angle/dihedrals. As a
> result, what I would have thought was that the simulation of C2H4 molecule
> in vacuum will not depend on the charges defined for each atom. If the
> parametrization of the H-C-C-H dihedral was done to reproduce the QM
> energy, the atomic charges should not have any effect on the energy. The
> atomic charges will be important if the simulation is done in a solvent.

You are correct - except that the fit to the QM energy for the H-C-C-H
dihedral was not done for strictly the dihedral term. The sequence of events
is to do the RESP fit to get the charges. Then when you calculate the
torsion profile in the QM code what you actually fit to that is the 1-4 EEL
and VDW energy + the dihedral energy. The only variables in this equation
are the parameters to the dihedral term since the charges are defined (and
fixed) by RESP.

Note, however that I have seen many times where people try to fit their own
parameters and they produce a nice QM dihedral profile and then just fit the
dihedral term to this (forgetting all about including the 1-4 EEL and VDW
terms as well). Hence what they actually think they have fitted to they have
not and when they then include it in a large simulation they don't realize
that their actual force field parameters are bogus since they forgot the 1-4

As for why they are calculated in the first place... I think this is a
historical aspect of how the original force fields were defined - perhaps
one of the force field guru's can comment on this - do you really need to
include the 1-4 EEL and VDW terms in your force field fits in order to
produce a decent force field?

I assume that the main advantage of keeping the 1-4 EEL and VDW terms is
that it reduces the complexity that you need in terms of the dihedral
parameters, I.e. it allows you to use wild cards in the form X - C - N - X -
where the 1-4 interactions are subtly different for different X's due to
them having different charges or VDW's. However, I don't know if anyone has
actually 'proven' this rather than it just being an arbitrary decision of
historical significance...

Comments anyone?

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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