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.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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Received on Wed Sep 20 2006 - 06:07:14 PDT
