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Improving the Wang-Landau algorithm for polymers and proteins
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Swetnam, Adam D. and Allen, M. P. (2010) Improving the Wang-Landau algorithm for polymers and proteins. Journal of Computational Chemistry, Volume 32 (Number 5). pp. 816-821. doi:10.1002/jcc.21660 ISSN 0192-8651.
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Official URL: http://dx.doi.org/10.1002/jcc.21660
Abstract
The 1/t Wang–Landau algorithm is tested on simple models of polymers and proteins. It is found that this method resolves the problem of the saturation of the error present in the original algorithm for lattice polymers. However, for lattice proteins, which have a rough energy landscape with an unknown energy minimum, it is found that the density of states does not converge in all runs. A new variant of the Wang–Landau algorithm that appears to solve this problem is described and tested. In the new variant, the optimum modification factor is calculated in the same straightforward way throughout the simulation. There is only one free parameter for which a value of unity appears to give near optimal convergence for all run lengths for lattice homopolymers when pull moves are used. For lattice proteins, a much smaller value of the parameter is needed to ensure rapid convergence of the density of states for energies discovered late in the simulation, which unfortunately results in poor convergence early on in the run.
| Item Type: | Journal Article | ||||
|---|---|---|---|---|---|
| Subjects: | Q Science > QC Physics | ||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Physics | ||||
| Library of Congress Subject Headings (LCSH): | Monte Carlo method, Polymers, Proteins | ||||
| Journal or Publication Title: | Journal of Computational Chemistry | ||||
| Publisher: | John Wiley & Sons, Inc. | ||||
| ISSN: | 0192-8651 | ||||
| Official Date: | 15 April 2010 | ||||
| Dates: |
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| Volume: | Volume 32 | ||||
| Number: | Number 5 | ||||
| Page Range: | pp. 816-821 | ||||
| DOI: | 10.1002/jcc.21660 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Restricted or Subscription Access | ||||
| Funder: | Engineering and Physical Sciences Research Council (EPSRC) |
Data sourced from Thomson Reuters' Web of Knowledge
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