Ross,
Is there any reason why the 1-4 EEL and VDW are calculated in the amber
force field (and in the other force fields)? As you said, in the eel and
vdw calculations, the 1-2 and 1-3 terms are never included, and 1-4
interactions are scaled and then included in the final EEL/VDW terms. I
never understood why the 1-4 interactions are included in the EEL and VDW
terms.
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.
Best regards,
On Fri, 21 Nov 2008, Ross Walker wrote:
> Hi Carlo,
>
> > I would like to ask a question that probably you will
> > consider trivial. What is the difference between the
> > energy components 1-4 EEL and EELEC ?
>
> I don't consider this a trivial question in fact I think no MD paper makes a
> good job of actually explaining how the force field works. For example most
> people write the AMBER or CHARMM force fields incorrectly in that they
> include the sum over VDW and electrostatics to be over all atoms within a
> cut off. However, they forget that this summation actually has an exclusion
> list associated with it.
>
> Essentially VDW and EEL interactions are NOT calculated between 1-2 (bonds)
> and 1-3 (angles) atoms that are covalently bonded. The reason for this is
> that these interactions are effectively parameterized into the bond and
> angle terms. A similar situation exists with the dihedral interactions
> except here the complete VDW and electrostatic interactions are not included
> within the parameterization of the dihedral term. However, calculating the
> full electrostatic and VDW interaction for 1-4 bonded atoms can make it
> difficult to obtain the desired behavior and so in the current AMBER force
> fields (GAFF, FF99SB, FF03 etc) the 1-4 interactions are calculated but then
> scaled by scee for electrostatics and scnb for VDW.
>
> Hence everything that is not bonded or separated by more than 3 bonds is
> included in the full electrostatic and VDW interaction as you see in the
> force field equation. All 1-2 and 1-3 interactions are skipped and all 1-4
> interactions are divided by 1.2 for EEL and 2.0 for VDW. (Note these values
> are a function of the way the force field was parameterized and so should
> never be changed - for example GLYCAM06 does no scaling of 1-4 terms and so
> these values are set to 1.0).
>
> Hence in order to do this the code first builds a direct space list of pair
> wise interactions and then subtracts from this list all 1-2, 1-3 and 1-4
> pairs. It then calculates the EEL and VDW terms which is what you see in the
> output as EELEC and VDWAALS (note in periodic simulations the PME EEL also
> ends up in EELEC). Then when doing the dihedral calculations for each unique
> 1-4 term it also calculates EEL and VDW and scales the energy and forces
> appropriately. This energy could then simply be added to the EELEC and
> VDWAALS terms but for troubleshooting etc it is instead reported separately
> as 1-4 EEL.
>
> > Why is
> > the EEL 1-4 term usually positive while EELEC is
> > generally negative ?
>
> I think that the 1-4 term being generally positive is a function of the
> typical distribution of charges around atoms separated by 3 bonds, there is
> certainly no requirement for it to be positive. Note though that the actual
> interaction between such atoms is really a function of both the 1-4 terms
> and the dihedral terms.
>
> > I also noticed that if I add together EEL 1-4 and EELEC,
> > this correlation with EGB becomes weaker. Why is it so?
>
> I'm not sure about this and others might be able to comment more on this but
> the main point is that the force field here isn't strictly pairwise
> decomposable, I.e. the 1-4 term also has a component to it that is
> parameterized into the dihedral term.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
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--
Ilyas Yildirim, Ph.D.
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Received on Fri Dec 05 2008 - 16:17:41 PST
