LIN - A NEW ALGORITHM TO SIMULATE THE DYNAMICS OF BIOMOLECULES BY COMBINING IMPLICIT-INTEGRATION AND NORMAL-MODE TECHNIQUES

A central goal in molecular dynamics simulations is increasing the int egration time-step to allow the capturing of biomolecular motion on bi ochemically interesting time frames. We previously made a step in that direction by developing the Langevin/implicit-Euler scheme. Here, we present a modified Langevin/implicit-Euler formulation for molecular d ynamics. The new method still maintains the major advantage of the ori ginal scheme, namely, stability over a wide range of time-steps. Howev er, it substantially reduces the damping effect of the high-frequency modes inherent in the original implicit scheme. The new formulation in volves separation of the solution into two components, one of which is solved exactly using normal-mode techniques, the other of which is so lved by implicit numerical integration. In this way, the high-frequenc y and fast-varying components are well resolved in the analytic soluti on component, while the remaining components of the motion are obtaine d by a large time-step integration phase. Full details of the new sche me are presented, accompanied by illustrative examples for a simple pe ndulum system. An application to liquid butane demonstrates stability of the simulations at time-steps up to 50 fs, still with activation of the high-frequency modes. (C) 1993 by John Wiley & Sons, Inc.