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
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Author: Carlos Sosa and T. Hewitt, (CRAY) and David Case, (SCRIPPS)
Email: someone@microsoft.com |