Table of Contents
Journal of Atomic, Molecular, and Optical Physics
Volume 2012, Article ID 782806, 6 pages
http://dx.doi.org/10.1155/2012/782806
Research Article

Accurate Calculation of the Density of States near the Ground-State Energy of the Peptides Met-Enkephalin and (Alanine)5 with the Wang-Landau Method: Lessons Learned

1School of Physical Science, Jawaharlal Nehru University, New Delhi 110067, India
2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India

Received 16 December 2011; Revised 7 March 2012; Accepted 7 March 2012

Academic Editor: Jan Petter Hansen

Copyright © 2012 Priya Singh and Pradipta Bandyopadhyay. 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.

Linked References

  1. F. Wang and D. P. Landau, “Efficient, multiple-range random walk algorithm to calculate the density of states,” Physical Review Letters, vol. 86, no. 10, pp. 2050–2053, 2001. View at Publisher · View at Google Scholar · View at Scopus
  2. P. Poulain, F. Calvo, R. Antoine, M. Broyer, and Ph. Dugourd, “Performances of Wang-Landau algorithms for continuous systems,” Physical Review E, vol. 73, no. 5, Article ID 056704, 11 pages, 2006. View at Publisher · View at Google Scholar · View at Scopus
  3. A. N. Morozov and S. H. Lin, “Accuracy and convergence of the Wang-Landau sampling algorithm,” Physical Review E, vol. 76, no. 2, Article ID 026701, 7 pages, 2007. View at Publisher · View at Google Scholar · View at Scopus
  4. N. Rathore, T. A. Knotts, and J. J. de Pablo, “Density of states simulations of proteins,” Journal of Chemical Physics, vol. 118, no. 9, pp. 4285–4290, 2003. View at Publisher · View at Google Scholar · View at Scopus
  5. P. Ojeda, M. E. Garcia, A. Londoño, and N. Y. Chen, “Monte carlo simulations of proteins in cages: influence of confinement on the stability of intermediate states,” Biophysical Journal, vol. 96, no. 3, pp. 1076–1082, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. C. Gervais, T. Wust, D. P. Landau, and Y. Xu, “Application of the Wang-Landau algorithm to the dimerization of glycophorin A,” Journal of Chemical Physics, vol. 130, no. 21, Article ID 215106, 7 pages, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. P. Singh, S. K. Sarkar, and P. Bandyopadhyay, “Understanding the applicability and limitations of Wang–Landau method for biomolecules: Met-enkephalin and Trp-cage,” Chemical Physics Letters, vol. 514, no. 4–6, pp. 357–361, 2011. View at Publisher · View at Google Scholar
  8. D. Barettin and P. Sibani, “Entropic algorithms and the lid method as exploration tools for complex landscapes,” Physical Review E, vol. 84, no. 3, Article ID 036706, 7 pages, 2011. View at Google Scholar
  9. U. H. E. Hansmann and Y. Okamoto, “Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem,” Journal of Computational Chemistry, vol. 14, no. 11, pp. 1333–1338, 1993. View at Publisher · View at Google Scholar
  10. R. E. Belardinelli and V. D. Pereyra, “Fast algorithm to calculate density of states,” Physical Review E, vol. 75, no. 4, Article ID 046701, 5 pages, 2007. View at Publisher · View at Google Scholar
  11. U. H. E. Hansmann, “Parallel tempering algorithm for conformational studies of biological molecules,” Chemical Physics Letters, vol. 281, no. 1–3, pp. 140–150, 1997. View at Google Scholar · View at Scopus
  12. Y. Sugita and Y. Okamoto, “Replica-exchange molecular dynamics method for protein folding,” Chemical Physics Letters, vol. 314, no. 1-2, pp. 141–151, 1999. View at Google Scholar · View at Scopus
  13. C. Junghans and U. H. E. Hansmann, “Numerical comparison of Wang-Landau sampling and parallel tempering for met-enkephalin,” International Journal of Modern Physics C, vol. 17, no. 6, pp. 817–824, 2006. View at Publisher · View at Google Scholar · View at Scopus
  14. G. Nemethy, K. D. Gibson, K. A. Palmer et al., “Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides,” Journal of Physical Chemistry, vol. 96, no. 15, pp. 6472–6484, 1992. View at Google Scholar · View at Scopus
  15. F. Eisenmenger, U. H. E. Hansmann, S. Hayryan, and C. K. Hu, “[SMMP] A modern package for simulation of proteins,” Computer Physics Communications, vol. 138, no. 2, pp. 192–212, 2001. View at Publisher · View at Google Scholar · View at Scopus
  16. L. Zhan, J. Z. Y. Chen, and W. K. Liu, “Conformational study of Met-enkephalin based on the ECEPP force fields,” Biophysical Journal, vol. 91, no. 7, pp. 2399–2404, 2006. View at Publisher · View at Google Scholar · View at Scopus