AMBER Archive (2006)

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

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Mon Sep 18 2006 - 21:16:20 CDT

> 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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