Molecular Dynamics

Introduction
Molecular dynamics is the science of simulating the motions of a system of particles. The essential elements for a molecular dynamics simulation are a knowledge of (1) the interaction potential (i.e., potential energy) for the particles, from which the forces can be calculated, and (2) the equations of motion governing the dynamics of the particles.

In molecular modeling, Newton's equations of motion are used. From energy minimization, one has the positions of, and forces on, the atoms. From the positions and forces, the accelerations on the particles can be obtained from Newton's second law. Therefore, to carry out a molecular dynamics simulation, we need to treat time explicitly and give a suitable set of initial velocities to the atoms. That is, molecular dynamics is used to animate the molecular model obtained from energy minimization.

Whereas each cycle of energy minimization can be thought of as a step in conformation space, each cycle of molecular dynamics advances in time through a very small step Dt. When this is repeated many times, the algorithm numerically integrates the equations of motion, producing a simulated trajectory in phase space.

On-Line Text
A good introduction to molecular dynamics that includes a discussion of the equations of motion and their integration is provided in the NIH Guide to Molecular Modeling.

Printed References
Case, D.A. (1993) Computer Simulations of Protein Dynamics and Thermodynamics, Computer/CS&E, October: 47-57.

Doniach, S. and Eastman, P. (1999) Protein Dynamics Simulations from Nanoseconds to Microseconds. Curr. Opin. Struct. Biol. 9: 157-163.

Gerstein, M. and Levitt, M. (1998) Simulating Water and the Molecules of Life. Sci. Am. , November: 100-105.

Hansson, T., Oostenbrink, C., and van Gunsteren, W.F. (2002) Molecular Dynamics Simulations. Curr. Opin. Struct. Biol. 12: 190-196.

Karplus, M. (2002) Molecular Dynamics Simulations of Biomolecules. Acct. Chem. Res. 35: 321-323.

Karplus, M. and Petsko, G.A. (1990) Molecular Dynamics Simulations in Biology. Nature 347: 631-639.

Karplus, M. and McCammon, J.A. (2002) Molecular Dynamics Simulations of Biomolecules, Nature Struct. Biol. 9: 646-652.

van Gunsteren, W.F. and Mark, A.E. (1992) On the Interpretation of Biochemical Data by Molecular Dynamics Computer Simulation, Eur. J. Biochem. 204: 947-961.

van Gunsteren, W.F., Hunenberger, P.H., Mark, A.E., Smith, P.E., and Tironi, I.G. (1995) Computer Simulation of Protein Motion, Comput. Phys. Commun. 91: 305-319.

Wang, W., Donini, O., Reyes, C.M., and Kollman, P.A. (2001) Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Initeractions. Annu. Rev. Biophys. Biomol. Struct. 30: 211-243.