Issue: 42
2005


THEORETICAL STUDY OF BIOMOLECULES BY MOLECULAR DYNAMICS SIMULATIONS
Alina Butu
pp. 31-46

Molecular dynamics simulations yield the possibility of describing and understanding the relationships between the structure and the function of biomolecules. This can be a very powerful tool to predict quantities that either cannot be measured directly or accurate experimental data are difficult to obtain. It provides a microscopic picture which may serve to explain macroscopic behaviour of a molecular system. Molecular dynamics can be applied to: sampling configuration space, e.g., simulated annealing to determine or refine structures; obtaining a description of the system at equilibrium, i.e., sampling with appropriate Boltzmann factor (structural and motional properties and values of thermodynamic parameters); obtaining actual dynamics and kinetics, i.e., sampling with appropriate Boltzmann factor and correct representation of the development of the system over time.