Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem

Abstract

We compare a few variants of the recently proposed multicanonical method with the well known simulated annealing for the effectiveness in search of the energy global minimum of a biomolecular system. For this we study in detail Met-enkephalin, one of the simplest peptides. We show that the new method not only outperforms simulated annealing in the search of the energy groundstate but also provides more statistical-mechanical information about the system.

to be published in Physica A, LATEX 32 pages, figures available on request

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• Thermodynamic Properties of the Dipolar Spin Ice Model
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• Finite-size scaling of helix-coil transitions in poly-alanine studied by multicanonical simulations
• Partition Function Zeros and Finite Size Scaling of Helix-Coil Transitions in a Polypeptide
• Characteristic Temperatures of Folding of a Small Peptide
• Formation of helical states in wormlike polymer chains
• Order-by-Disorder in the XY Pyrochlore Antiferromagnet Revisited
• Multicanonical Methods vs. Molecular Dynamics vs. Monte Carlo: Comparison for Lennard-Jones Glasses
• Simulated Annealing with Tsallis Weights - A Numerical Comparison
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• Thermodynamics and Kinetics of Folding of a Small Peptide
• Protofold II: Enhanced Model and Implementation for Kinetostatic Protein Folding
• An Introduction to Monte Carlo Simulation of Statistical physics Problem
• The Folding Funnel Landscape of the Peptide Met-enkephalin
• Enhanced Sampling Algorithms