TCB Publications - Abstract

Andreas Windemuth and Klaus Schulten. Stochastic dynamics simulation for macromolecules. Beckman Institute Technical Report TB-91-19, University of Illinois, 1991.

WIND91B A new method for the simulation of macromolecules is proposed. The method is derived from classical Newtonian Dynamics by the substitution of random variables for atomic velocities. It combines features of both Newtonian Dynamics and Monte-Carlo simulation and reproduces the time scale of motion correctly. The resulting dynamics is equivalent to solving the Langevin equation of an overdamped system, obeys the Einstein relation and corresponds to a canonical ensemble description. We argue that the probability distribution for the positions of atoms is reproduced better than by Newtonian dynamics, due to a neglect of quantum effects in the latter. The stochastic nature of the proposed algorithm allows numerical restrictions on the length of integration intervals to be relaxed and simulation times to be extended beyond those of the Verlet algorithm for Newtonian Dynamics. The method underestimates, however, cross correlations of atomic velocities that give rise to concerted inertial motions of groups of atoms.

Download Full Text

The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper's publisher and author. You may not upload any of this site's material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Reproduction or storage of materials retrieved from this web site is subject to the U.S. Copyright Act of 1976, Title 17 U.S.C.

Download full text: PDF ( 1.1MB)