next up previous
Next: Classical Simulation and Modeling Up: Matching CHARMM's Electrostatic Approximations Previous: Partial Solvation by Explicit

Solutions, Crystals, and Interfaces

Solutions and crystals are simulated as `infinite' systems. More precisely, the basic `unit cell' (e.g., a single protein in a cube of water) having zero net charge is replicated periodically in all three dimensions. Periodic boundary conditions are used so that an atom exiting through one face of the unit cell enters the cell through the opposite face. These simulations are expensive, requiring considerable explicit water and the calculation of forces exerted by the `image' atoms that neighbor the primary unit cell. Ewald summation is the preferred electrostatic treatment for these periodic systems. If an interface (e.g., air-water) is present, Ewald summation may improve results even more than otherwise.

Peter J. Steinbach 2010-11-15