Home | About Journal | Web Links | E-mail Alerts | RSS RSS Icon | Browse
Previous Article Next Article

An efficient umbrella potential for the accurate calculation of free energies by molecular simulation

Source: J. Chem. Phys. 133, 044115 (2010); doi:10.1063/1.3464330

Published 29 July 2010

KEYWORDS and PACS
Keywords
PACS
  • 05.70.Ce
    Thermodynamic functions and equations of state
  • 31.10.+z
    Theory of electronic structure, electronic transitions, and chemical binding in atoms and molecules
  • 34.20.-b
    Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
  • YEAR: 2010
RELATED DATABASES

To view database links for this article,
you need to log in.
To view database links for this article,
you need to log in.
PUBLICATION DATA
ISSN:
1553-9628 (online)
Publisher:
AIP is a member of CrossRef AIP
Di Wu
Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China and CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200433, China
Umbrella sampling has been widely used to calculate free energies in many chemical and biological applications because it can effectively bridge the systems of interest and sample in the united phase space that is essential to yield accurate results. Many algorithms have implemented the idea of umbrella sampling that greatly improves the calculation of free energies. An efficient umbrella potential not only can connect the systems of interest, but also can lower the energetic barriers and facilitate the sampling over the relevant phase spaces. Here we present such an umbrella potential that is built on the equations of the weighted histogram analysis method. The proposed umbrella potential can facilitate the sampling of the important phase spaces of the systems of interest, which ensures the accurate calculation of free energies. We test this umbrella potential using a harmonic-model system, a water system, and a Lennard-Jones system. We demonstrate that this umbrella potential is effective in the circumstances when the systems of interest do not exhibit overlap in their phase spaces. ©2010 American Institute of Physics
History: Received 7 January 2010; accepted 24 June 2010; published 29 July 2010
Permalink: http://link.aip.org/link/?JCPSA6/133/044115/1

REFERENCES (26)

For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University, New York, 1987)
  2. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed. (Academic, San Diego, 2002)
  3. D. A. Kofke, Mol. Phys. 102, 405 (2004)
  4. Fluid Phase Equilib. 228–229, 41 (2005)
  5. H. Meirovitch, Curr. Opin. Struct. Biol. 17, 181 (2007)
  6. R. J. Radmer and P. A. Kollman, J. Comput. Chem. 18, 902 (1997)
  7. F. M. Ytreberg, R. H. Swendsen, and D. M. Zuckerman, J. Chem. Phys. 125, 184114 (2006).
  8. R. W. Zwanzig, J. Chem. Phys. 22, 1420 (1954).
  9. D. Wu and D. A. Kofke, J. Chem. Phys. 123, 054103 (2005).
  10. D. Wu and D. A. Kofke, J. Chem. Phys. 123, 084109 (2005).
  11. G. M. Torrie and J. P. Valleau, Chem. Phys. Lett. 28, 578 (1974).
  12. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977).
  13. M. Mezei, J. Comput. Phys. 68, 237 (1987)
    14. P. Virnau and M. Muller, J. Chem. Phys. 120, 10925 (2004).
  14. R. Radhakrishnan and T. Schlick, J. Chem. Phys. 121, 2436 (2004).
  15. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988).
  16. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
  17. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992)
    18. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, ibid. 16, 1339 (1995).
  18. C. H. Bennett, J. Comput. Phys. 22, 245 (1976).
  19. B. A. Berg and T. Neuhaus, Phys. Rev. Lett. 68, 9 (1992).
  20. A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsovvelyaminov, J. Chem. Phys. 96, 1776 (1992).
  21. F. A. Escobedo and C. R. A. Abreu, J. Chem. Phys. 124, 104110 (2006)
    22. F. A. Escobedo and F. J. Martinez-Veracoechea, ibid. 129, 154107 (2008).
  22. C. Jarzynski, Phys. Rev. E 56, 5018 (1997)
    23. Phys. Rev. Lett. 78, 2690 (1997).
  23. N. D. Lu, D. Wu, T. B. Woolf, and D. A. Kofke, Phys. Rev. E 69, 057702 (2004)
    24. S. X. Sun, J. Chem. Phys. 118, 5769 (2003)
    D. Wu and D. A. Kofke, ibid. 122, 204104 (2005).
  24. F. G. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001)
    25. Phys. Rev. E64, 056101 (2001).
  25. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, J. Chem. Phys. 119, 9406 (2003)
    26. Q. L. Yan and J. J. de Pablo, Phys. Rev. Lett. 90, 035701 (2003).
  26. C. D. Christ and W. F. van Gunsteren, J. Chem. Phys. 126, 184110 (2007)
    27. E. Lyman and D. M. Zuckerman, ibid. 127, 065101 (2007)
    J. S. Wang and R. H. Swendsen, J. Stat. Phys. 106, 245 (2002).
  27. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
  28. D. Wu, J. Chem. Phys. 128, 224105 (2008).
  29. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997)
    30. B. Roux, Comput. Phys. Commun. 91, 275 (1995).
  30. F. A. Escobedo and F. J. Martinez-Veracoechea, J. Chem. Phys. 127, 174103 (2007).
  31. D. Wu and D. A. Kofke, Phys. Rev. E 70, 066702 (2004).
  32. J. Hermans, A. Pathiaseril, and A. Anderson, J. Am. Chem. Soc. 110, 5982 (1988).

CITING ARTICLES
For access to citing articles, you need to log in.
For access to citing articles, you need to Log in.
ADVERTISEMENT