SC is the International Conference for
 High Performnance Computing, Networking, Storage and Analysis

SCHEDULE: NOV 13-19, 2010

Non-Equilibrium Umbrella Sampling on Blue Gene/P using One-Sided Communication

SESSION: Research Poster Reception

EVENT TYPE: Poster

TIME: 5:15PM - 7:00PM

AUTHOR(S):Alex Dickson, Jeff R. Hammond, Aaron R. Dinner

ROOM:Main Lobby

ABSTRACT:
In molecular simulations, important dynamics are often dominated by rare events. In such cases, reaction rates and transition states can be obtained by parallel sampling of phase space by regions. Nonequilibrium umbrella sampling (NEUS) is appropriate for systems driven far from equilibrium. In this poster we describe the first massively-parallel implementation of NEUS using Global Arrays. Efficient strong-scaling to 8192 processors of BlueGene/P is demonstrated for a coarse-grained, 262-residue RNA segment under explicit flow modeled with stochastic rotation dynamics. This approach can be used to scale explicit-atom molecular dynamics rare event simulations to many petaflops. Preliminary results show that the flow-extended RNA molecule can visit different meta-stable states, whose relative probabilities depend strongly on the pressure that drives the flow of the solvent. These developments suggest that the parallel version of NEUS will be a powerful tool to examine rare events in large nonequilibrium systems.

Chair/Author Details:

Alex Dickson - University of Chicago

Jeff R. Hammond - Argonne National Laboratory

Aaron R. Dinner - University of Chicago

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