Scalable Time-Parallelization of Molecular Dynamics Simulations in Nano Mechanics

— 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 (  ¢¡¤£¦¥¨§ ) seconds. Therefore, a large number of iterations are required to reach realistic time scales. In fact, this is acknowledged as the major bottleneck in MD. While parallelization has been effective for dealing with the computational effort that arises in simulating large systems (that is, having a large number of atoms), conventional parallelization is not effective in simulating small physical systems to long time scales. Such simulations are often required for evaluating the physical, mechanical, and chemical properties at micro and nano scales. We recently introduced a new approach to parallelization, through guided simulations, where data from related prior simulations are used to parallelize a new computation alon...

• Type: Conference
• Year: 2006
• Where: ICPP
• Authors: Yanan Yu, Ashok Srinivasan, Namas Chandra
• Keywords: Distributed And Parallel Computing, ICPP 2006, Physical Systems, Prior Simulations, Time Scales