Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.
Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.
Hamelberg
Donald
D
NSF Center for Theoretical Biological Physics and Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093-0365, USA. dhamelbe@mccammon.ucsd.edu
Mongan
John
J
McCammon
J Andrew
JA
D001665:Binding Sites; D019295:Computational Biology; D003198:Computer Simulation; D004735:Energy Transfer; D008954:Models, Biological; D013816:Thermodynamics