Title: Long-Time Molecular Dynamics Simulations in Nano-mechanics through Parallelization of the Time Domain

Molecular Dynamics (MD) is an important atomistic simulation technique, with widespread use in computational chemistry, biology, and materials. An important limitation of MD is that the time step size is typically restricted to the order of femto (10^{-15}) seconds. Therefore a large number of iterations are required to reach realistic time scales. In fact, this is acknowledged as a major bottleneck in MD. While parallelization has been effective for dealing with the computational effort that arises in simulating large systems, conventional parallelization is not effective in simulating small or moderate sized physical systems to long time scales. We will present a new approach to parallelization that we recently introduced, where data from related simulations are used to parallelize a computation along the time domain. In this work, we use time parallelization to simulate a Carbon Nanotube, consisting of just around 1000 atoms, using MD, on up to 1000 processors with close to ideal speedups. In contrast, spatial decomposition is not effective on more than 2-3 processors. The significance of this work lies in demonstrating the effectiveness of a new parallelization approach that can enable MD simulations to reach long time-scales, using massively parallel machines.

Ashok Srinivasan
Assistant Professor
Dept. of Computer Science
Florida State University

Phone: (850) 644-0559
Fax: (850) 644-0058
Email: asriniva@cs.fsu.edu
URL: www.cs.fsu.edu/~asriniva
253 Love Building Office: 169 Love Building
Tallahassee FL 32306-4530