𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Accelerating molecular dynamic simulation on the cell processor and Playstation 3

✍ Scribed by Edgar Luttmann; Daniel L. Ensign; Vishal Vaidyanathan; Mike Houston; Noam Rimon; Jeppe Øland; Guha Jayachandran; Mark Friedrichs; Vijay S. Pande

Publisher
John Wiley and Sons
Year
2009
Tongue
English
Weight
94 KB
Volume
30
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

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

📜 SIMILAR VOLUMES

Accelerating molecular dynamic simulatio
Accelerating molecular dynamic simulation on graphics processing units
✍ Mark S. Friedrichs; Peter Eastman; Vishal Vaidyanathan; Mike Houston; Scott Legr 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 624 KB

## Abstract We describe a complete implementation of all‐atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimization

Molecular dynamics simulations of aqueou
Molecular dynamics simulations of aqueous ions at the liquid–vapor interface accelerated using graphics processors
✍ Brad A. Bauer; Joseph E. Davis; Michela Taufer; Sandeep Patel 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 291 KB

## Abstract Molecular dynamics (MD) simulations are a vital tool in chemical research, as they are able to provide an atomistic view of chemical systems and processes that is not obtainable through experiment. However, large‐scale MD simulations require access to multicore clusters or supercomputer

A simple algorithm to accelerate the com
A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations
✍ Pedro Gonnet 📂 Article 📅 2006 🏛 John Wiley and Sons 🌐 English ⚖ 149 KB

## Abstract Cell lists are ubiquitous in molecular dynamics simulations—be it for the direct computation of short‐range inter‐atomic potentials, the short‐range direct part of a long‐range interaction or for the periodic construction of Verlet lists. The conventional approach to computing pairwise

Protein calculations on parallel process
Protein calculations on parallel processors. II. Parallel algorithm for the forces and molecular dynamics
✍ J.F. Janak; P.C. Pattnaik 📂 Article 📅 1992 🏛 John Wiley and Sons 🌐 English ⚖ 456 KB

## Abstract We describe two algorithms for the parallel calculation of a CHARMm‐like force field in macromolecules. For a molecule with a given number of atoms, we show that there is an optimal number of processors leading to a minimum computation time. At the optimum, both the number of processors

Molecular dynamics simulations and free
Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase
✍ Stephanie B. A. De Beer; Alice GlÄttli; Johannes Hutzler; Nico P. E. Vermeulen; 📂 Article 📅 2011 🏛 John Wiley and Sons 🌐 English ⚖ 382 KB

## Abstract 4‐Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied