Skip to main content
SpringerLink
Log in

Calculating Free Energy Differences Using Perturbation Theory

  • Chapter
Book cover Free Energy Calculations

Part of the book series: Springer Series in CHEMICAL PHYSICS ((CHEMICAL,volume 86))

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 299.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 379.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 379.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Born, M., Volumen und Hydratationswarme der Ionen, Z. Phys. 1920, 1, 45-48

    Article  CAS  Google Scholar 

  2. Kirkwood, J. G., Statistical mechanics of fluid mixtures, J. Chem. Phys. 1935, 3, 300-313

    Article  CAS  Google Scholar 

  3. Zwanzig, R. W., High-temperature equation of state by a perturbation method. I. Nonpolar gases, J. Chem. Phys. 1954, 22, 1420-1426

    Article  CAS  Google Scholar 

  4. Jorgensen, W. L.; Ravimohan, C., Monte Carlo simulation of differences in free energies of hydration, J. Chem. Phys. 1985, 83, 3050-3054

    Article  CAS  Google Scholar 

  5. Simonson, T.; Archontis, G.; Karplus, M., Free energy simulations come of age: protein-ligand recognition, Acc. Chem. Res. 2002, 35, 430-437

    Article  CAS  Google Scholar 

  6. Shing, K. S.; Gubbins, K. E., The chemical potential in dense fluids and fluid mixtures via computer simulation, Mol. Phys. 1982, 46, 1109-1128

    Article  CAS  Google Scholar 

  7. Kenney, J. F.; Keeping, E. S., Mathematics of Statistics, [2nd edition], Van Nostrand: Princeton, NJ, 1951

    Google Scholar 

  8. Hummer, G.; Pratt, L.; Garcia, A. E., Free energy of ionic hydration, J. Phys. Chem. 1996,100,1206-1215

    Article  CAS  Google Scholar 

  9. H ünenberger, P. H.; McCammon, J. A., Ewald artifacts in computer simulations of ionic solvation and ion-ion interactions: a continuum electrostatics study, J. Chem. Phys. 1999,110,1856-1872

    Article  Google Scholar 

  10. Markus, Y., J. Chem. Soc. Faraday Trans. 1991, 87, 2995-2999

    Article  Google Scholar 

  11. Pohorille, A.; Chipot, C.; New, M.; Wilson, M. A. Molecular modeling of protocellular functions, in Pacific Symposium on Biocomputing ’96, Hunter, L.; Klein, T. E., Eds. World Scientific: Singapore, 1996, pp. 550-569

    Google Scholar 

  12. Onsager, L., Electric moments of molecules in liquids, J. Am. Chem. Soc. 1936, 58, 1486-1493

    Article  CAS  Google Scholar 

  13. Pearlman, D. A.; Kollman, P. A., A new method for carrying out free energy perturba-tion calculations: dynamically modified windows, J. Chem. Phys. 1989, 90, 2460-2470

    Article  CAS  Google Scholar 

  14. Lu, N.; Kofke, D. A., Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling, J. Chem. Phys. 2001, 114, 7303-7312

    Article  CAS  Google Scholar 

  15. Kollman, P. A., Free energy calculations: Applications to chemical and biochemical phenomena, Chem. Rev. 1993, 93, 2395-2417

    Article  CAS  Google Scholar 

  16. King, P. M. Free energy via molecular simulation: A primer. in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Van Gunsteren, W. F.; Weiner, P. K.; Wilkinson, A. J., Eds., vol. 2. ESCOM: Leiden, 1993, pp. 267-314

    Google Scholar 

  17. Kollman, P. A., Advances and continuing challenges in achieving realistic and predic-tive simulations of the properties of organic and biological molecules, Acc. Chem. Res. 1996,29,461-469

    Article  CAS  Google Scholar 

  18. Kal é , L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K., NAMD 2: Greater scalability for parallel molecular dynamics, J. Comput. Phys. 1999, 151, 283-312

    Article  Google Scholar 

  19. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L., Com-parison of simple potential functions for simulating liquid water, J. Chem. Phys. 1983, 79,926-935

    Article  CAS  Google Scholar 

  20. Pohorille, A.; Benjamin, I., Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface. A molecular dynamic study, J. Phys. Chem. 1993, 97, 2664-2670

    Article  CAS  Google Scholar 

  21. Chipot, C.; Wilson, M. A.; Pohorille, A., Interactions of anesthetics with the water-hexane interface. A molecular dynamics study, J. Phys. Chem. B 1997, 101, 782-791

    Article  CAS  Google Scholar 

  22. Silin, V.; Plant, A., Biotechnological applications of surface plasmon resonance, Trends Biotechnol. 1997, 15, 353-359

    Article  CAS  Google Scholar 

  23. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A., The statistical-thermodynamic basis for computation of binding affinities: a critical review, Biophys. J. 1997, 72, 1047-1069

    Article  CAS  Google Scholar 

  24. Hermans, J.; Wang, L., Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme, J. Am. Chem. Soc. 1997, 119, 2707-2714

    Article  CAS  Google Scholar 

  25. Liu, S. Y.; Mark, A. E.; van Gunsteren, W. F., Estimating the relative free energy of different molecular states with respect to a single reference state, J. Phys. Chem. 1996, 100,9485-9494

    Article  CAS  Google Scholar 

  26. Oostenbrink, C.; van Gunsteren, W. F., Free energies of ligand binding for structurally diverse compounds, Proc. Natl Acad. Sci. USA 2005, 102, 6750-6754

    Article  CAS  Google Scholar 

  27. Pearlman, D. A., A comparison of alternative approaches to free energy calculations, J. Phys. Chem. 1994, 98, 1487-1493

    Article  CAS  Google Scholar 

  28. Bash, P. A.; Singh, U. C.; Langridge, R.; Kollman, P. A., Free energy calculations by computer simulation, Science 1987, 236, 564-568

    Article  CAS  Google Scholar 

  29. Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex, Science 1987, 235,574-576

    Article  CAS  Google Scholar 

  30. Pearlman, D. A.; Kollman, P. A., The overlooked bond-stretching contribution in free energy perturbation calculations, J. Chem. Phys. 1991, 94, 4532-4545

    Article  CAS  Google Scholar 

  31. Wang, L.; Hermans, J., Change of bond length in free-energy simulations: algorithmic improvements, but when is it necessary?, J. Chem. Phys. 1994, 100, 9129-9139

    Article  CAS  Google Scholar 

  32. Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M., Hidden thermodynamics of mutant proteins: a molecular dynamics analysis, Science 1989, 244, 1069-1072

    Article  CAS  Google Scholar 

  33. Boresch, S.; Karplus, M., The role of bonded terms in free energy simulations: I. Theo-retical analysis, J. Phys. Chem. A 1999, 103, 103-118

    Article  CAS  Google Scholar 

  34. Boresch, S.; Karplus, M., The role of bonded terms in free energy simulations: II. Cal-culation of their influence on free energy differences of solvation, J. Phys. Chem. A 1999,103,119-136

    Article  CAS  Google Scholar 

  35. Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F., Avoiding singularities and neumerical instabilities in free energy calculations based on molecular simulations, Chem. Phys. Lett. 1994, 222, 529-539

    Article  CAS  Google Scholar 

  36. Lee, C. Y.; Scott, H. L., The surface tension of water: A Monte Carlo calculation using an umbrella sampling algorithm, J. Chem. Phys. 1980, 73, 4591-4596

    Article  CAS  Google Scholar 

  37. Bennett, C. H., Efficient estimation of free energy differences from Monte Carlo data, J. Comp. Phys. 1976, 22, 245-268

    Article  Google Scholar 

  38. Hansmann, U. H. E., Parallel tempering algorithm for conformational studies of biolog-ical molecules, Chem. Phys. Lett. 1997, 281, 140-150

    Article  CAS  Google Scholar 

  39. Fukunishi, O. Watanabe; Takada, S., On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction, J. Chem. Phys. 2002, 116, 9058-9067

    Article  CAS  Google Scholar 

  40. Hummer, G.; Pratt, L.; Garcia, A. E., Multistate Gaussian model for electrostatic solva-tion free energies, J. Am. Chem. Soc. 1997, 119, 8523-8527

    Article  CAS  Google Scholar 

  41. Szeg ö, G., Orthogonal Polynomials, [4th edition], American Mathematical Society: Providence, 1975

    Google Scholar 

  42. Andrews, G. E.; Askey, R.; Roy, R., Special Functions, Cambridge University Press: Cambridge, 1999

    Google Scholar 

  43. Sivia, D. S., Data Analysis. A Bayesian Tutorial, Clarendon: Oxford, 1996

    Google Scholar 

  44. Sansone, G., Orthogonal Functions, Dover: New York, 1991

    Google Scholar 

  45. Amadei, A.; Apol, M. E. F.; Berendsen, H. J. C., The quasi-Gaussian entropy theory: free energy calculations based on the potential energy distribution function, J. Chem. Phys. 1996, 104, 1560-1574

    Article  CAS  Google Scholar 

  46. Bramwell, S. T.; Christensen, K.; Fortin, J. Y.; Holdsworth, P. C. W.; Jensen, H. J.; Lise, S.; L ópez, J. M.; Nicodemi, M.; Pinton, J. F.; Sellitto, M., Universal fluctuations in correlated systems, Phys. Rev. Lett. 2000, 84, 3744-3747

    Article  CAS  Google Scholar 

  47. Nanda, H.; Lu, N.; Kofke, D. A., Using non-Gaussian density functional fits to improve relative free energy calculations, J. Chem. Phys. 2005, 122, 134110:1-8

    Google Scholar 

  48. Pearlman, D. A.; Rao, B. G. Free energy calculations: Methods and applications. in Encyclopedia of computational chemistry, Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer III, H. F.; Schreiner, P. R., Eds., vol. 2. Wiley: Chichester, 1998, pp. 1036-1061

    Google Scholar 

  49. Fleischman, S. H.; Brooks III, C. L., Thermodynamics of aqueous solvation: solution properties of alchohols and alkanes, J. Chem. Phys. 1987, 87, 3029-3037

    CAS  Google Scholar 

  50. Lu, N.; Kofke, D. A.; Woolf, T. B., Staging is more important than perturbation method for computation of enthalpy and entropy changes in complex systems, J. Phys. Chem. B 2003, 107, 5598-5611

    Article  CAS  Google Scholar 

  51. H énin, J.; Pohorille, A.; Chipot, C., Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A., J. Am. Chem. Soc. 2005, 127, 8478-8484

    Article  Google Scholar 

  52. Smith, P. E.; van Gunsteren, W. F., Predictions of free energy differences from a single simulation of the initial state, J. Chem. Phys. 1994, 100, 577-585

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Equipe de Dynamique des Assemblages Membranaires UMR CNRS/UHP 7565, Universite Henri Poincare, BP 239, 54506, Vandoe uvre-l s-Nancy cedex, France

    Christophe Chipot

  2. Department of Pharmaceutical Chemistry, University of California San Francisco, 94143, San Francisco, California

    Andrew Pohorille

Authors
  1. Christophe Chipot
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrew Pohorille
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Equipe de Dynamique des Assemblages Membranaires UMR CNRS/UHP 7565, Universite Henri Poincare, BP 239, 54506, Vandoe uvre-l s-Nancy cedex, France

    Christophe Chipot

  2. Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, CA 94143, San Francisco, USA

    Andrew Pohorille

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Chipot, C., Pohorille, A. (2007). Calculating Free Energy Differences Using Perturbation Theory. In: Chipot, C., Pohorille, A. (eds) Free Energy Calculations. Springer Series in CHEMICAL PHYSICS, vol 86. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-38448-9_2

Download citation

Publish with us

Policies and ethics

Search

Navigation