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Algorithms 2009, 2(1), 215-226; doi:10.3390/a2010215

Automatic Determination of Stepsize Parameters in Monte Carlo Simulation Tested on a Bromodomain-Binding Octapeptide

1
Department of Physiology and Biophysics and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York 10021, USA
2
Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU, New York, NY 10029, USA
*
Author to whom correspondence should be addressed.
Received: 30 October 2008 / Revised: 7 January 2009 / Accepted: 24 January 2009 / Published: 10 February 2009
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
View Full-Text   |   Download PDF [170 KB, uploaded 10 February 2009]

Abstract

The proportional integral controller, commonly used in engineering applications for process control, has been implemented for the tuning of the stepsizes in Metropolis Monte Carlo simulations. Similarly to the recent application for tuning the chemical potential parameter in grand-canonical ensemble simulation, the process-control approach was found to work well for the problem of selecting the stepsize for each torsion angle that results in a targeted acceptance rate during the simulation of an octapeptide in aqueous environment.
Keywords: Monte Carlo; acceptance rate; stepsize; process control Monte Carlo; acceptance rate; stepsize; process control
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Banfelder, J.R.; Speidel, J.A.; Mezei, M. Automatic Determination of Stepsize Parameters in Monte Carlo Simulation Tested on a Bromodomain-Binding Octapeptide. Algorithms 2009, 2, 215-226.

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