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Accelerating molecular dynamic simulation on the cell processor and Playstation 3.

Edgar Luttmann¹, Daniel L Ensign, Vishal Vaidyanathan

¹Department of Chemistry, Stanford University, Stanford, California 94305, USA.

Journal of Computational Chemistry

|July 11, 2008

Summary

Accelerating molecular dynamics (MD) simulations using novel algorithms on the Cell processor significantly enhances computational power for complex systems. This research demonstrates improved performance over traditional processors for physical property calculations.

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Area of Science:

Computational chemistry
High-performance computing

Background:

Molecular dynamics (MD) simulations are crucial for calculating physical properties of complex systems.
Novel hardware architectures can potentially accelerate these computationally intensive simulations.

Purpose of the Study:

To detail algorithmic advances for accelerating MD simulations on the Cell processor.
To explore the suitability of streaming processors for specific MD calculations, such as implicit solvation models.

Main Methods:

Development of specialized algorithms for the Cell processor architecture.
Analysis of memory access patterns versus computational load.
Focus on optimizing implicit solvation models for streaming processors.

Main Results:

Significant performance improvements in MD simulations on the Cell processor compared to traditional architectures.
Identification of computational tasks best suited for the Cell processor's streaming capabilities.

Conclusions:

The Cell processor, with optimized algorithms, offers a powerful platform for accelerating molecular dynamics simulations.
Algorithmic advancements are key to leveraging novel architectures for enhanced physical property calculations.