Development of an Atomistic Brownian Dynamics Algorithm with Implicit Solvent Model for Long Time Simulation

Tadashi ANDO, Toshiyuki MEGURO and Ichiro YAMATO*

Department of Biological Science and Technology, Tokyo University of Science
2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan

(Received: June 6, 2002; Accepted for publication: July 23, 2002; Published on Web: September 13, 2002)

We report the implementation of an atomistic Brownian dynamics simulation of proteins. A protein was described by united-atom model with AMBER91 force field. The solvent was treated by distance-dependent dielectric/surface area model. The computation time of the Brownian dynamics and the calculated results on structure and dynamics of 28-mer bba fold peptide with the implicit solvent model were compared with those of molecular dynamics simulation with explicit solvent. The Brownian dynamics simulation was 53 times faster than molecular dynamics simulation with explicit solvent. The simulation was stable and the artifacts often observed in simulations at vacuum condition were reduced. The results indicate that the Brownian dynamics with the implicit solvent model can be widely used in studies of protein dynamics by long time simulation in future.

Keywords: Brownian dynamics, implicit solvent model, distance-dependent dielectric, surface area

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