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.
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