Speaker: Dr. Mark E. Tuckerman
From: Department of Chemistry and Courant Institute of Mathematical Sciences -
New York University - New York, NY
Date / Time / Room: Friday, April 22, 2005 / 10:30 - 11:30 AM/Room 124 Center for Social Concerns

Title: Molecular dynamics with a 100 fs time step: Non-Hamiltonian dynamics and phase space analysis as a solution to the resonance problem

Abstract: Biological macromolecules are characterized by a wide range of time scales ranging over 12-15 orders of magnitude from a few tens of femtoseconds, representing, for example, C-H and N-H bond stretching to the millisecond-second time scale for the formation of biologically active folded structures in proteins and nucleic acids. Bridging these time scales is a major challenge in the theoretical modeling of biological systems. Currently, molecular dynamics calculations, one of the most widely used approaches, are fundamentally limited in their time discretization parameter or time step to a few femtoseconds by so called resonance phenomena that arise when multiple time scale integration techniques are employed. In this talk, it will be shown how non-Hamiltonian equations of motion can be employed to overcome resonance problems, thereby allowing time steps as large as 100 fs or more to be used in simulations based on all-atom force €elds. In the course of this talk, techniques for analyzing the phase space distribution generated by non-Hamiltonian dynamical systems will be reviewed and applied to show that, despite the large time steps employed, the correct distribution is obtained. Applications to exible water models and large proteins in vacuo will be presented.