Discrete molecular dynamics

Abstract

AbstractDiscrete molecular dynamics (DMD) has emerged as a simplification of traditional molecular dynamics (MD). DMD employs discrete step function potentials in place of the continuous potential used in traditional MD. As a result, the simulation engine solves the ballistic equations of motion for only those particles participating in a collision, instead of solving Newton's equations of motion for every particle in the system. Because fewer calculations are performed per time step, the DMD technique allows for longer time and length scales to become accessible in the simulation of large biomolecules. The use of coarse‐grained models extends the computational advantage of this method. Although some accuracy is sacrificed to speed, because of the usefulness of DMD to the simulation of many particles at longer timescales, the technique has seen application to diverse molecular systems. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 80–92 DOI: 10.1002/wcms.4This article is categorized under: Structure and Mechanism > Molecular Structures Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods