Drude particle

Drude particles are model oscillators used to simulate the effects of electronic polarizability in the context of a classical molecular mechanics force field. It is based on the Drude model of mobile electrons. Molecular mechanics models, commonly used for computational calculations such as structural minimization and molecular dynamics simulations, represent individual atoms or other particles as hard spheres that interact according to the laws of Newtonian mechanics. These methods are often used in the computational study of proteins, nucleic acids, and other biomolecules.

Most force fields in current practice use a fixed-charge model in which each atom in the simulation is assigned a single electric charge that does not change during the course of the simulation. This obviously cannot model induced dipoles or other electronic effects of a changing local environment. Drude particles are massless virtual sites carrying partial electric charge and attached to individual atoms via a harmonic spring. The spring constant and relative partial charges on the atom and associated Drude particle determine the extent to which the Drude particle responds to the local electrostatic field. The movement of the Drude particle thus serves as a proxy for the changing distribution of the electric charge associated with the corresponding atom.^[1]

The Drude particle method, and polarizable force fields in general, have not yet been widely applied due to their very high computational cost compared to the equivalent fixed-charge simulation. In the Drude model, this cost is largely due to the challenge in recalculating the local electrostatic field and repositioning the Drude particles at each time step; traditionally this is done using an iterative self consistent field (SCF) method, although a much more efficient method has been developed that assigns a very small mass to each Drude particle and applies a Lagrangian transformation.^[2] Water models incorporating Drude sites have also been developed^[3] and refined for incorporation into a polarizable force field under development.^[4]

References

1. ^ MacKerell AD. (2004). Empirical force fields for biological macromolecules: Overview and issues. J Comp Chem 25(13): 1584-1604.
2. ^ Lamoureux G, Roux B. (2003). Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm. J Chem Phys 119(6):3025-3039.
3. ^ Lamoureux G, MacKerell AD, Roux B. (2003). A simple polarizable model of water based on classical Drude oscillators. J Chem Phys 119(3):5185-97.
4. ^ Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD. (2006). A polarizable model of water for molecular dynamics simulations of biomolecules. Chem Phys Lett 418:245-9.