Efficient molecular dynamics using geodesic integration and solvent-solute splitting.
We present an approach to Langevin dynamics in the presence of holonomic constraints based on decomposition of the system into components representing geodesic flow, constrained impulse and constrained diffusion. We show that a particular ordering of the components results in an integrator that is an order of magnitude more accurate for configurational averages than existing alternatives. Moreover, by combining the geodesic integration method with a solvent-solute force splitting, we demonstrate that stepsizes of at least 8 fs can be used for solvated biomolecules with high sampling accuracy and without substantially altering diffusion rates, approximately increasing by a factor of two the efficiency of molecular dynamics sampling for such systems. The methods described in this article are easily implemented using the standard apparatus of modern simulation codes.
School of Mathematics and Maxwell Institute of Mathematical Sciences, University of Edinburgh , James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
Benedict
B
Leimkuhler
Department of Statistics , University of Chicago , 5734 S. University Avenue, Chicago, IL 60637, USA.
Charles
0000-0001-9545-1346
C
Matthews
Brownian dynamics; Langevin dynamics; biomolecular simulation; constrained molecular dynamics; high-dimensional sampling; stochastic differential equations