Skip to main content

Formal Aspects of the Potential of Mean Force Approach

  • Conference paper
Computation of Biomolecular Structures

Abstract

During the last seven years, we have developed and tested a method for treating solvent effects on biomolecules in aqueous solution which we call the Potentials of Mean Force (PMF) approach.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight 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

  • Abernethy GM, Gillan (1980) A new method of solving the HNC equation for ionic liquids. Mol.Phys.4:839–847

    Article  Google Scholar 

  • Allen MP, Tildesley DJ (1987) Computer Simulation of Liquids.Clarendon Press Oxford

    Google Scholar 

  • Andersen HC, Chandler D (1972a) Optimized Cluster Expansions for Classical Fluids II. General Theory and Variational Formulation of the Mean Spherical Model and Hard Sphere Percus-Yevick equations. J.Chem.Phys.57:1918–1929

    Article  CAS  Google Scholar 

  • Andersen HC, Chandler D, Weeks JD (1972b) Optimized Cluster Expansions for Classical Fluids III. Applications to Ionic Solutions and Simple Liquids. J.Chem.Phys. 57:2626–2631

    Article  CAS  Google Scholar 

  • Barker JA, Henderson D (1971) Monte-Carlo values for the radial distribution of a system of fluid hard spheres. Mol.Phys.21:187–191

    Article  CAS  Google Scholar 

  • Barker JA, Henderson D (1976) What is a liquid? Understanding the states of matter. Rev.Mod.Phys.48:578–671

    Article  Google Scholar 

  • Belloni L (1985) A Hypernetted Chain Study of highly asymmetrical polyelectrolytes. Chem.Phys.99:43–54

    Article  CAS  Google Scholar 

  • De Dominicis C (1962) Variational Formulations of Equilibrium Statistical Mechanics. J.Math.Phys.5:983–1002

    Article  Google Scholar 

  • Frisch HL, Lebowitz JL (eds) (1964) The Equilibrium Theory of Classical Fluids. Benjamin New York

    Google Scholar 

  • Garcia AE, Soumpasis DM (1989) Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution. Proc.Natl.Acad.Sci.USA 86:3160–3164

    Article  PubMed  CAS  Google Scholar 

  • Garcia AE, Gupta G, Soumpasis DM, Tung CS (1990) Energetics of the hairpin to mismatched duplex transition of dGCCGCAGC. J.Biomol.Struct.&Dyn.8:173–186

    CAS  Google Scholar 

  • Hansen JP, McDonald JR (1990) Theory of simple Fluids.2nd edition. Academic Press London etc

    Google Scholar 

  • Hill TL (1956) Statistical Mechanics. Principles and selected Applications. McGraw-Hill New York etc

    Google Scholar 

  • Hummer G, Soumpasis DM (1992) An Extended RISM Study of Simple Electrolytes:Pair Correlations in a NaCl-SPC Water Model. Mol.Phys.75:633–651

    Article  CAS  Google Scholar 

  • Hummer G, Soumpasis DM, Neumann M (1992) Pair Correlations in a NaCl-SPC Water Model. Simulations versus extended RISM computations. Mol.Phys. (in press)

    Google Scholar 

  • Klement R, Soumpasis DM, von Kitzing E, Jovin TM (1990) Inclusion of Ionic Interactions in Force Field Calculations of Charged Biomolecules-DNA Structural Transitions. Biopolymers 29:1089–1103

    Article  PubMed  CAS  Google Scholar 

  • Klement R, Soumpasis DM, Jovin TM (1991) Computation of ionic distributions around charged biomolecular structures:Results for right handed and left handed DNA. Proc.Natl.Acad.Sci.USA 88:4631–4635

    Article  PubMed  CAS  Google Scholar 

  • Kirkwood JG (1935) Statistical Mechanics of Fluid Mixtures. J.Chem.Phys.3:300–313

    Article  CAS  Google Scholar 

  • McMillen WG, Mayer JE (1945) The Statistical Thermodynamics of Multicomponent Systems. J.Chem.Phys.13:276–305

    Article  Google Scholar 

  • Meeron E (1960) Nodal Expansions.III.Exact Integral Equations for Particle Correlation Functions. J.Math.Phys.1:192–201

    Article  Google Scholar 

  • Montroll E, Lebowitz JL (eds) (1982) The Liquid State of Matter: Fluids, Simple and Complex. North-Holland Amsterdam

    Google Scholar 

  • Morita T (1959) Theory of Classical Fluids: Hyper-Netted Chain Approximation.III. A New Integral Equation for the Pair Distribution Function. Prog.Theor.Phys.23:829–845

    Article  Google Scholar 

  • Morita T,Hiroike K (1961) A New Approach to the Theory of Classical Fluids.III. General Treatnent of Classical Systems. Prog.Theor.Phys.25:537–578

    Article  Google Scholar 

  • Muenster A (1969) Statistical Thermo dynamics. Vols 1 & 2. Springer Berlin Heidelberg New York

    Google Scholar 

  • Soumpasis DM (1984) Statistical mechanics of the B-Z transition of DNA: contribution of diffuse ionic interactions. Proc.Natl.Acad.Sci.USA 81:5116–5120

    Article  PubMed  CAS  Google Scholar 

  • Soumpasis DM, Wiechen J, Jovin TM (1987a) Relative Stabilities and Transitions of DNA Conformations in 1:1 Electrolytes A theoretical Study. J.Biom.Struct.& Dyn.4:535–552

    CAS  Google Scholar 

  • Soumpasis DM, Robert-Nicoud M, Jovin TM (1987b) B-Z conformational transition in 1:1 electrolytes: dependence upon counterion size. FEBS Lett.213:341–344

    Article  PubMed  CAS  Google Scholar 

  • Soumpasis DM (1988) Salt dependence of DNA structural stabilities in solution: Theoretical predictions versus experiments. J.Biom.Struct. & Dyn.6:563–574

    CAS  Google Scholar 

  • Soumpasis DM, Garcia AE, Klement R, Jovin TM (1991) in; Theoretical Biochemistry & Molecular Biophysics. Beveridge DL, Lavery R (eds) Vol 1 Adenine Press Guilder-land NY:343–360

    Google Scholar 

  • Van Leewen JMJ, Groeneveld J, De Boer J (1959) New Method for the Calculation of the Pair Correlation Function.I Physica 25:792–808

    Google Scholar 

  • Verlet L, Weis JJ (1972) Equilibrium Theory of Simple Liquids. Phys.Rev.A5:939–952

    Google Scholar 

  • Waisman E, Lebowitz JL (1972a) Mean Spherical Model Integral Equation for Charged Hard Spheres.I. Method of Solution. J.Chem.Phys.56:3086–3092

    Article  CAS  Google Scholar 

  • Waisman E, Lebowitz JL (1972b) Mean Spherical Model Intrgral Equation for Charged Hard Spheres.II. Results. J.chem.Phys. 56:3093–3100

    Article  CAS  Google Scholar 

  • Weiner PK, Kollman P, Cuse U, Singh C, Ohio G, Alogerma S, Profeta JR, Weiner P (1984) A New Force Field for Molecular Mechanical Simulation of Nuclein Acids and Proteins. J.Am.Chem Soc.l06:765–784

    Article  Google Scholar 

  • Wiechen J (1980) Diplomarbeit. Freie Universitaet Berlin

    Google Scholar 

  • Zerah G (1985) An efficient Newton’s Method for the Numerical Integration of Fluid Integral Equations. J.Comp.Phys. 61:280–285

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1993 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Soumpasis, D.M. (1993). Formal Aspects of the Potential of Mean Force Approach. In: Soumpasis, D.M., Jovin, T.M. (eds) Computation of Biomolecular Structures. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-77798-1_16

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-77798-1_16

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-77800-1

  • Online ISBN: 978-3-642-77798-1

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics