Department of

Computational Biological Chemistry

Polarizable MD simulations

Molecular charge distributions change in response to the local environment. Quantum-mechanics can describe this effect but corresponding simulations are very limited in size and time. Classical simulations are traditionally performed with permanent partial charges. Polarizability models can bridge this gap by augmenting the permanent charge distribution by satellite charges (Drude model corresponding to a induced physical dipole) or additional point-induced dipoles (mathematical dipoles).

Model Method Stringency CPU time
non-polarizable 1.4 h
point-induced dipoles LAG Tμ=0.06 2.0 h
Drudes LAG Tμ=1 2.7 h

The point-induced dipole method augments the standard set of coordinates (representative of the nuclear degrees of freedom) by a set of atomic dipoles which are intended to represent the electronic degrees of freedom. Since the strength of this induced dipole depends on the local electric field of all others, the polarization forces are not pairwise additive anymore, but are true many-body forces.

In the Drude model, the induced dipoles are represented by additional charged satellites which are tethered by a "spring" to the polarizable atom. The strength of this spring is related to the atomic polarizability. In principle, one obtains the position of the mobile Drude particles by a self-consistent field approach, but a Lagrangian approach with two thermal baths is faster and as reliable as the self-consistent field.

The atomic polarizability reflects the sensitiveness of the atom to changes in the electric field. Their macroscopic analogue -- which is not their sum -- determines the optical dielectric constant or the square of the refractive index. In this way the polarizabilities can be calibrated. While being of intrinsically local diversity the inclusion of polarizability accelerates molecular dynamics.


Imprint: (as stipulated by Austrian law, MedienG 2005): S. Boresch / C. Schröder,
Institut für Computergestützte Biologische Chemie, Währinger Strasse 17, 1090 Wien, Austria