AMBER Archive (2008)

Subject: Re: AMBER: Electrostatic Energy Components

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Nov 21 2008 - 17:46:10 CST

well the rotational barriers have a large steric and elec component to
them, so you want these interactions. for most dihderals they are
really the only major thing going on. the torsion profile (in
principle) is only for corrections of the orbital effects. we scale
the 1-4s because they do have a through-bond component and are thus
not purely the classical barrier. over time these have been used more
as empirical corrections rather than just for the quantum effects.
hope that helps
carlos

On Fri, Nov 21, 2008 at 5:33 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> 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
> contributions.
>
> 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
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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