Chapter 20.2 Molecular-dynamics simulations of biological macromolecules

Abstract

Advances in the theory of atomic interactions and the increasing availability of high-power computers have led to rapid development of the molecular-dynamics field and greater understanding of macromolecular motions. It is now practical to use molecular dynamics, in combination with crystallographic and NMR data, to search the large conformational space of proteins and nucleic acids to find structures consistent with the data and to improve the agreement with the data. The topics covered in this chapter include: the simulation method; potential-energy functions; empirical parameterization of the force field; modifications in the force field for structure determination; internal dynamics and average structures; assessment of the simulation procedure; and effect of crystallographic atomic resolution on structural stability during molecular-dynamics simulation. Keywords: force fields; molecular dynamics; particle-mesh Ewald method; potential-energy functions; restraints