On Incorporating Multiple Timestep Methods
into Particle Mesh Ewald for Biomolecular Simulations

 

DANNY BARASH, LINJING YANG, XIAOLIANG QIAN, AND TAMAR SCHLICK
Department of Chemistry
and Courant Institute of Mathematical Sciences
New York University
New York, NY 10003, USA
barash@biomath.nyu.edu

[ poster ]

Abstract:

We present a multiple-time step force splitting scheme for Particle Mesh Ewald, developed for use in the AMBER program. We analyze the advantages and limitations of the new scheme. Based on our findings, we conclude that the contributor of instabilities in MTS/PME protocols - the intramolecular cancellation error - cannot easily be controlled to reap the full advantages from MTS algorithms. We thus suggest that the larger timesteps needed to make MTS algorithms advantageous can be accomplished by methods other than the PME for fast electrostatics.

[ abstract ]