Vectorization of the Generalized Born Method in AMBER

11/21/00

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Table of Contents

Vectorization of the Generalized Born Method in AMBER

Agenda

CRAY SV1 Target Applications

CRAY T3E Target Applications

Motivation

Solvent Effects

Simulations Limitations

Continuum Models

Discrete Hydration

Solvation Free Energy

Electrostatic Contribution to the Free Energy of Solvation

Generalized Born (GB) Equation

Non-electrostatic Contributions to the Solvation Energy

Generalized Born Routine Optimization

Original Loop 200

Loop 200 Step 1

CRAY SV1 Architectural Features

Single CPU Performance

Myoglobin Single CPU Performance on a CRAY SV1

Mflops versus Number of Atoms for Four Different Proteins

Myoglobin Multiple CPU Performance on CRAY SV1

Summary

Future Work

Acknowledgements

Author: Carlos Sosa and T. Hewitt, (CRAY) and David Case, (SCRIPPS)

Email: someone@microsoft.com