AMBER Archive (2006)

Subject: RE: [UCE]Re: RE: AMBER: potential energy

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Sep 18 2006 - 23:01:04 CDT

Dear Fenghui,

Consider the calculation of a simple complex A + B -> AB

We have:

PE of A = Energy of A + zero point of A
PE of B = Energy of B + zero point of B

PE of AB = Energy of A* + Energy of B* + zero point of A + zero point of B

Where * represents the configuration in the complex.

Binding energy is then

( PE of A + PE of B ) - PE of AB

expanding this out we get

( Energy of A + zero point of A + Energy of B + zero point of B ) - (Energy
of A* + Energy of B* + zero point of A + zero point of B)

=

(Energy of A + Energy of B) - (Energy of A* + Energy of B*)

So as you see the zero point energies here cancel out.

The important point to remember that everything you are calculating is
concerned with delta-energies. E.g. the delta between A and A*. In all these
cases the zero points (or origins) cancel out and are not an issue.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Fenghui Fan
> Sent: Monday, September 18, 2006 19:41
> To: amber_at_scripps.edu
> Subject: Re: [UCE]Re: RE: AMBER: potential energy
>
> But how about MM-PBSA? For the protein, ligand and the
> protein-ligand comples should have something in common
>
> and comparable on energy. So what will be their 0
> point for each component of the energy?
>
> Best regards.
>
> Fenghui Fan
>
> -
> --- Thomas Cheatham <tec3_at_utah.edu> wrote:
>
> >
> > > Usually kineticn energy >0
> > > and potential energy <0
> > > and total erngy <0 for most system.
> > > however if we met the case below
> > > kineticn energy >0
> > > and potential energy <0
> > > and total erngy >0 ******
> > > does this MD simulation valid or not.
> >
> > Short answer to your question (building on what Ross
> > Walker said): The
> > potential energy is relative. We do not have a
> > set/known zero point for
> > each molecule, or equivalently, you cannot directly
> > compare molecular
> > mechanics potential energies for different
> > molecules. It does not matter
> > whether the total potential energy is positive or
> > negative, nor does the
> > value directly relate to its stability compared to
> > other molecules as the
> > zero point could be positive, negative or zero
> > depending on the
> > parameterization.
> >
> > Some additional points. The terms for the bonds and
> > angles are harmonic
> > and therefore always zero or positive. Torsions are
> > typically positive,
> > however there is no restriction in the code that
> > disallows a negative
> > force constant. Negative potential energy values
> > typically come from the
> > pairwise potential and will depend on how strong the
> > van der Waals
> > attraction is (assuming limited repulsion) and the
> > balance of the charges.
> >
> > With the standard force fields we use, and TIP3P
> > water, typically the
> > electrostatics is large and negative. However, if
> > you used the TIP3SP
> > model as parameterized in CHARMM, the energy is
> > typically "higher" due to
> > the inclusion of a vdw repulsion term on the water
> > hydrogens (absent in
> > TIP3P). The energy change running with these two
> > potentials does not
> > state anything about the relative stability of the
> > respective MD
> > simulations; they just have different energy zero
> > points.
> >
> >
> >
> >
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