Implementation of Molecular Dynamics and Its Extensions with the Coarse- Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics

A Liwo and S Oldziej and C Czaplewski and DS Kleinerman and P Blood and HA Scheraga, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6, 890-909 (2010).

DOI: 10.1021/ct9004068

We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures. In addition to coarse-grained parallelism already implemented in our previous work, in which each conformation was treated by a different task, we introduce a fine-grained level in which energy and gradient evaluation are split between several tasks. The Message Passing Interface (MPI) libraries have been utilized to construct the parallel code. The parallel performance of the code has been tested on a professional Beowulf cluster (Xeon Quad Core), a Cray XT3 supercomputer, and two IBM BlueGene/P supercomputers with canonical and replica- exchange molecular dynamics. With IBM BlueGene/P, about 50% efficiency and a 120-fold speed-up of the fine-grained part was achieved for a single trajectory of a 767-residue protein with use of 256 processors/trajectory. Because of averaging over the fast degrees of freedom, UNRES provides an effective 1000-fold speed-up compared to the experimental time scale and, therefore, enables us to effectively carry out millisecond-scale simulations of proteins with 500 and more amino acid residues in days of wall-clock time.

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