Accelerating molecular dynamic simulation on the cell processor and Playstation 3

Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009

[1]  Pengyu Y. Ren,et al.  Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation , 2003 .

[2]  Samuel Williams,et al.  The potential of the cell processor for scientific computing , 2005, CF '06.

[3]  V. Pande,et al.  Absolute comparison of simulated and experimental protein-folding dynamics , 2002, Nature.

[4]  Martin Hopkins,et al.  Synergistic Processing in Cell's Multicore Architecture , 2006, IEEE Micro.

[5]  SugermanJeremy,et al.  Brook for GPUs , 2004 .

[6]  Xavier Barril,et al.  Molecular modelling. , 2006, Molecular bioSystems.

[7]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[8]  Vijay S. Pande,et al.  Screen Savers of the World Unite! , 2000, Science.

[9]  B. Montgomery Pettitt,et al.  Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids , 1985 .

[10]  Regine Herbst-Irmer,et al.  High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Klaus Schulten,et al.  Accelerating Molecular Modeling Applications with GPU Computing , 2009 .

[12]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[13]  Laxmi N. Bhuyan,et al.  High-performance computer architecture , 1995, Future Gener. Comput. Syst..

[14]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[15]  Pat Hanrahan,et al.  Brook for GPUs: stream computing on graphics hardware , 2004, SIGGRAPH 2004.

[16]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[17]  Themis Lazaridis,et al.  Distance and exposure dependent effective dielectric function , 2002, J. Comput. Chem..

[18]  A. Spada,et al.  Crystal structures of human factor Xa complexed with potent inhibitors. , 2000, Journal of medicinal chemistry.

[19]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[20]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[21]  D. Case,et al.  Modification of the Generalized Born Model Suitable for Macromolecules , 2000 .

[22]  O. Steinhauser,et al.  Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. The reaction field method. , 1992, Journal of molecular biology.

[23]  P. Kollman,et al.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.

[24]  J. Ramstein,et al.  Energetic coupling between DNA bending and base pair opening. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Peijuan Zhu,et al.  Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth‐permittivity finite difference Poisson–Boltzmann method , 2004, J. Comput. Chem..

[26]  P. Bahadur,et al.  Principles of Polymer Science , 2002 .

[27]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[28]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[29]  Karl F Freed,et al.  All‐atom fast protein folding simulations: The villin headpiece , 2002, Proteins.