Copernicus: A new paradigm for parallel adaptive molecular dynamics.

S. Pronk, P. Larson, I. Pouya, G. Bowman, I. Haque, K. Beaucamp, B. Hess, V. S. Pande, P. M. Kasson, E. Lindahl.

Supercomputing 2011, submitted (2011)

Biomolecular simulation is a core application on supercomputers, but it is exceptionally difficult to achieve the strong scaling necessary to reach biologically relevant timescales. Here, we present a new paradigm for parallel adaptive molecular dynamics and a publicly available implementation: Copernicus. This framework combines performance-leading molecular dynamics parallelized on three levels (SIMD, threads, and message-passing) with kinetic clustering, statistical model building and real-time result monitoring.

Copernicus enables execution as single parallel jobs with automatic resource allocation. Even for a small protein such as villin (9,864 atoms), Copernicus exhibits near-linear strong scaling from 1 to 5,376 AMD cores. Starting from extended chains we observe structures 0.6Å from the native state within 30h, and achieve sufficient sampling to predict the native state without a priori knowledge after 80-90h. To match Copernicus’ efficiency, a classical simulation would have to exceed 50μs per day, currently infeasible even with custom hardware designed for simulations.