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

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

1email, 1email and 2,* email
Received: 30 October 2008; in revised form: 7 January 2009 / Accepted: 24 January 2009 / Published: 10 February 2009
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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
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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.

AMA Style

Banfelder JR, Speidel JA, Mezei M. Automatic Determination of Stepsize Parameters in Monte Carlo Simulation Tested on a Bromodomain-Binding Octapeptide. Algorithms. 2009; 2(1):215-226.

Chicago/Turabian Style

Banfelder, Jason R.; Speidel, Joshua A.; Mezei, Mihaly. 2009. "Automatic Determination of Stepsize Parameters in Monte Carlo Simulation Tested on a Bromodomain-Binding Octapeptide." Algorithms 2, no. 1: 215-226.

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