Free energy by molecular simulation

Reviews in Computational Chemistry

Volumn 9, Issue , 1996, Pages 81-127

  Straatsma, T P ^a,b  

^a University of Houston   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR STRUCTURE;

ELECTRONIC POLARIZATION; MOLECULAR SIMULATIONS; THERMODYNAMIC INTEGRATION; THERMODYNAMIC PERTURBATION;

FREE ENERGY;

EID: 0030503687     PISSN: 10693599     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (131)

1. D. A. McQuarrie, Statistical Thermodynamics, Harper & Row, New York, 1973.
2. L. E. Reichl, A Modern Course in Statistical Physics, Edward Arnold, Austin, TX, 1980.
3. J. P. M. Postma, H. J. C. Berendsen and J. R. Haak, Faraday Symp. Chem. Soc., 17, 55 (1982). Thermodynamics of Cavity Formation in Water.
4. B. L. Tembe and J. A. McCammon, Comput. Chem., 4, 281 (1984). Ligand-Receptor Interactions.
5. W. F. van Gunsteren and H. J. C. Berendsen, GROningen Molecular Simulation (GROMOS) Library Manual, Biomos, Nijenborgh 16, 9747 AG Groningen, The Netherlands, 1987.
6. T. P. Straatsma and J. A. McCammon, J. Comput. Chem., 11, 943 (1990). ARGOS, a Vectorized General Molecular Dynamics Program.
7. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187 (1983). CHARMM: A Program for Macromolecular Energy Minimization, and Dynamics Calculations.
8. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr., and P. Weiner, J. Am. Chem. Soc., 106, 765 (1984). A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins.
9. S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comput. Chem., 7, 230 (1986). An All-Atom Force Field for Simulations of Proteins and Nucleic Acids.
10. W. L. Jorgensen, J. Am. Chem. Soc., 106, 6638 (1984). Optimized Intermolecular Potential Functions for Liquid Hydrocarbons.
11. W. L. Jorgensen and J. Tirado-Rives, J. Am. Chem. Soc., 110, 1666 (1988). The OPLS Potential Functions for Proteins: Energy Minimizations for Crystals of Cyclic Peptides and Crambin.
12. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys., 21, 1087 (1953). Equation of State Calculations by Fast Computing Machines.
13. W. F. van Gunsteren and H. J. C. Berendsen, Angew. Chem. Int. Ed. Engl., 29, 992 (1990). Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry.
14. R. W. Zwanzig, J. Chem. Phys., 22, 1420 (1954). High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases.
15. P. Weiner and P. A. Kollman, J. Comput. Chem., 2, 287 (1981). AMBER: Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions.
16. M. J. Mitchell and J. A. McCammon, J. Comput. Chem., 12, 271 (1991). Free Energy Difference Calculations by Thermodynamic Integration: Difficulties in Obtaining a Precise Value.
17. W. L. Jorgensen and C. Ravimohan, J. Chem. Phys., 83, 3050 (1985). Monte Carlo Simulation of Differences in Free Energies of Hydration.
18. T. P. Straatsma and J. A. McCammon, J. Chem. Phys., 95, 1175 (1991). Multiconfiguration Thermodynamic Integration.
19. M. Mezei, J. Chem. Phys., 86, 7084 (1987). The Finite Difference Thermodynamic Integration, Tested on Calculating the Hydration Free Energy Difference between Acetone and Dimethylamine in Water.
20. M. Watanabe and W. P. Reinhardt, Phys. Rev. Lett., 65, 3301 (1990). Solvent Polarization and Hydration of the Chloride Anion.
21. J. Schlitter, Mol. Simulation, 7, 105 (1991). Methods for Minimizing Errors in Linear Thermodynamic Integration.
22. W. F. van Gunsteren, in Computer Simulation of Biomolecular Systems, W. F. van Gunsteren and P. K. Weiner, Eds., ESCOM, Leiden, 1989, pp. 27-59. Methods for Calculation of Free Energies and Binding Constants: Successes and Problems.
23. J. Gao, M. Karplus, K. Kuczera, and B. Tidor, Science, 244, 1069 (1989). Hidden Thermodynamics of Mutant Proteins. A Molecular Dynamics Analysis.
24. B. Tidor and M. Karplus, Biochemistry, 30, 3217 (1991). Simulation Analysis of the Stability Mutant R96H of T4 Lysozyme.
25. M. Prevost, S. J. Wodak, B. Tidor, and M. Karplus, Proc. Natl. Acad. Sci. U.S.A., 88, 880 (1991). Contribution of the Hydrophobic Effect to Protein Stability. Analysis Based on Simulations of the Ile-96-Ala Mutation in Barnase.
26. L. X. Dang, K. M. Merz Jr., and P. A. Kollman, J. Am. Chem. Soc., 111, 8505 (1989). Free Energy Calculations on Protein Stability: the Threonine 157 to Valine 157 Mutation of T4 Lysozyme.
27. U. C. Singh, Proc. Natl. Acad. Sci. U.S.A., 85, 4280 (1988). Probing the Salt Bridge in the Dihydrofolate Reductase Methotrexate Complex by Using the Coordinate Coupled Free Energy Perturbation Method.
28. U. C. Singh and S. J. Benkovic, Proc. Natl. Acad. Sci. U.S.A., 85, 9519 (1988). A Free Energy Perturbation Study of the Binding of Methotrexate to Mutants of Dihydrofolate Reductase.
29. S. Boresch, G. Archontis, and M. Karplus, Proteins: Struct. Funct. Genet., 20, 25 (1994). Free Energy Simulations: the Meaning of the Individual Contributions from a Component Analysis.
30. A. E. Mark and W. F. van Gunsteren, J. Mol. Biol., 240, 167 (1994). Decomposition of the Free Energy of a System in Terms of Specific Interactions. Implications for Theoretical and Experimental Studies.
31. M. Zacharias and T. P. Straatsma, Mol. Simulation, 14, 417 (1995). Path Dependence of Free Energy Components in Thermodynamic Integration.
32. C. L. Brooks III, Int. J. Quantum Chem., Quantum Biol. Symp., 15, 221 (1988). Thermodynamic Calculations on Biological Molecules.
33. C. L. Brooks III and S. H. Fleischman, J. Am. Chem. Soc., 112, 3307 (1990). A Theoretical Approach to Drug Design. I. Relative Solvation Thermodynamics for the Antibacterial Compound Trimethoprim and Ethyl Derivatives Substituted at the 3′, 4′ and 5′ Positions.
34. C. L. Brooks III, in Computer Modelling of Fluid Polymers and Solids, C. R. A. Catlow, Ed., Kluwer Academic Publishers, Dordrecht, 1990, pp. 289-334. Molecular Simulations of Protein Structure, Dynamics and Thermodynamics.
35. J. A. McCammon and S. C. Harvey, Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, 1987.
36. J. Kottalam and D. A. Case,J. Am. Chem. Soc., 110, 7690 (1988). Dynamics of Ligand Escape from the Heme Pocket of Myoglobin.
37. C. D. Bell and S. C. Harvey, J. Phys. Chem., 90, 6595 (1986). Comparison of Free Energy Surfaces for Extended Atom and All Atom Models of n-Butane.
38. R. Elber, J. Chem. Phys., 93, 4312 (1990). Calculation of the Potential of Mean Force Using Molecular Dynamics with Linear Constraints: An Application to a Conformational Transition in a Solvated Dipeptide.
39. J. van Eerden, W. J. Briels, S. Harkema, and D. Feil, Chem. Phys. Lett., 164, 370 (1989). Potential of Mean Force by Thermodynamic Integration: Molecular Dynamics Simulation of Decomplexation.
40. C. X. Wang, H. Y. Liu, Y. Y. Shi, and F. H. Huang, Chem. Phys. Lett., 179, 475 (1991). Calculations of Relative Free Energy Surfaces in Configuration Space Using an Integration Method.
41. M. Mezei, P. K. Mehrotra, and D. L. Beveridge, J. Am. Chem. Soc., 107, 2239 (1985). Monte Carlo Determination of the Free Energy and Internal Energy of Hydration for the Ala Dipeptide at 25 °C.
42. D. J. Tobias and C. L. Brooks III, Chem. Phys. Lett., 142, 472 (1987). Calculation of Free Energy Surfaces Using Methods of Thermodynamic Perturbation Theory.
43. D. J. Tobias and C. L. Brooks III, J. Chem. Phys., 89, 5115 (1988). Molecular Dynamics with Internal Coordinate Constraints.
44. D. J. Tobias, S. F. Sneddon, and C. L. Brooks III, J. Mol. Biol., 216, 783 (1991). Reverse Turns in Blocked Dipeptides Are Intrinsically Unstable in Water.
45. D. J. Tobias and C. L. Brooks III, Biochemistry, 30, 6059 (1991). Thermodynamics and Mechanism of α-Helix Initiation in Alanine and Valine Peptides.
46. W. F. van Gunsteren, Mol. Phys., 40, 1015 (1980). Constrained Dynamics of Flexible Molecules.
47. T. P. Straatsma, H. J. C. Berendsen, and J. P. M. Postma, J. Chem. Phys., 85, 6720 (1986). Free Energy of Hydrophobic Hydration: A Molecular Dynamics Study of Noble Gases in Water.
48. D. A. Pearlman and P. A. Kollman, J. Chem. Phys., 90, 2460 (1989). A New Method for Carrying Out Free Energy Perturbation Calculations: Dynamically Modified Windows.
49. A. E. Mark, W. F. van Gunsteren, and H. J. C. Berendsen, J. Chem. Phys., 94, 3808 (1991). Calculations of Relative Free Energy via Indirect Pathways.
50. D. A. Pearlman, J. Phys. Chem., 98, 1487 (1994). A Comparison of Alternative Approaches to Free Energy Calculations.
51. T. P. Straatsma, M. Zacharias, and J. A. McCammon, Chem. Phys. Lett., 196, 297 (1992). Holonomic Constraint Contributions to Free Energy Differences from Thermodynamic Integration Molecular Dynamics Simulations.
52. J. M. Depaepe, J. P. Ryckaert, E. Pad, and G. Ciccotti, Mol. Phys., 79, 515 (1993). Sampling of Molecular Conformations by Molecular Dynamics Techniques.
53. W. C. Swope and H. C. Andersen,J. Chem. Phys., 88, 6548 (1984). A Molecular Dynamics Method for Calculating the Solubility of Gases in Liquids and the Hydrophobic Hydration of Inert-Gas Atoms in Aqueous Solution.
54. M. Zacharias, T. P. Straatsma, and J. A. McCammon, J. Chem. Pbys., 100, 9025 (1994). Separation-Shifted Scaling, a New Scaling Method for Lennard-Jones Interactions in Thermodynamic Integration.
55. W. F. van Gunsteren and H. J. C. Berendsen, Mo. Phys., 34, 1311 (1977). Algorithms for Macromolecular Dynamics and Constraint Dynamics.
56. L. Wang and J. Hermans, J. Chem. Phys., 100, 9129 (1994). Change of Bond Length in Free Energy Simulations: Algorithmic Improvements, But When Is It Necessary?
57. D. A. Pearlman and P. A. KollmanJ. Chem. Phys., 94, 4532 (1990). The Overlooked Bond-Stretching Contribution in Free Energy Perturbation Calculations.
58. R. Edberg, D. J. Evans, and J. P. Morris, J. Chem. Phys., 84, 6933 (1986). Constrained Molecular Dynamics: Simulations of Liquid Alkanes with a New Algorithm.
59. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys., 23, 327 (1977). Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes.
60. H. J. C. Berendsen and W. F. van Gunsteren, in The Physics of Superionic Conductors and Electrode Materials, NATO ASI Series B: Physics, Vol. 92, J. W. Perran, Ed., Plenum Press, London, 1983, pp. 221-240. Molecular Dynamics with Constraints.
61. D. J. Tobias, C. L. Brooks III, and S. H. Fleischman, Chem. Phys. Lett., 156, 256 (1989). Conformational Flexibility in Free Energy Simulations.
62. T. P. Straatsma and J. A. McCammon, J. Chem. Phys., 90, 3300 (1989). Treatment of Rotational Isomers in Free Energy Evaluations. Analysis of the Evaluation of Free Energy Differences by Molecular Dynamics Simulations of Systems with Rotational Isomeric States.
63. A. G. Anderson and J. Hermans, Proteins, 3, 262 (1988). Microfolding: Conformational Probability Map for the Alanine Dipeptide in Water from Molecular Dynamics Simulation.
64. R.-H. Yun and J. Hermans, Protein Eng., 4, 761 (1991). Conformational Equilibria of Valine Studied by Dynamics Simulation.
65. J. Hermans, R.-H. Yun, and A. G. Anderson, in Crystallographic and Modeling Methods in Molecular Design, C. E. Bugg and S. E. Ealick, Eds., Springer-Verlag, New York, 1990, pp. 95-113. Stability of Folded Conformations by Computer Simulation: Methods and Some Applications.
66. R. H. Yun, A. G. Anderson, and J. Hermans, Proteins: Struct. Funct. Genet., 10, 219 (1991). Praline in α-Helix: Stability and Conformation Studied by Dynamics Simulation.
67. C. Haydock, J. C. Sharp, and F. G. Prendergast, Biophys. J., 57, 1269 (1990). Tryptophan-47 Rotational Isomerization in Variant-3 Scorpion Neurotoxin. A Combination Thermodynamic Perturbation and Umbrella Sampling Study.
68. T. P. Straatsma and J. A. McCammon, J. Chem. Phys., 101, 5032 (1994). Treatment of Rotational Isomeric States. III. The Use of Biasing Potentials.
69. T. C. Beutler and W. F. van Gunsteren,J. Chem. Phys., 100, 1492 (1994). The Computation of a Potential of Mean Force: Choice of the Biasing Potential in the Umbrella Sampling Technique.
70. F. Fraternali and W. F. van Gunsteren, Biopolymers, 34, 347 (1994). Conformational Transitions of a Dipeptide in Water: Effects of Imposed Pathways Using Umbrella Sampling Techniques.
71. T. P. Straatsma and J. A. McCammon, J. Chem. Phys., 91, 3631 (1989). Treatment of Rotational Isomers in Free Energy Calculations. II. Molecular Dynamics Simulation Study of 18-Crown-6 in Aqueous Solution as an Example of Systems with Large Numbers of Rotational Isomeric States.
72. D. A. Pearlman and P. A. Kollman, Biopolymers, 29, 1193 (1990). The Calculated Free Energy Effects of 5-Methylcytosine on the B to Z Transition in DNA.
73. C. L. Brooks III, J. Chem. Phys., 86, 5156 (1987). The Influence of Long Range Force Truncation on the Thermodynamics of Aqueous Ionic Solutions.
74. S. E. Huston and P. J. Rossky, J. Chem. Phys., 93, 7888 (1989). Free Energies of Association for the Sodium-Dimethyl Phosphate Ion Pair in Aqueous Solution.
75. C. Chipot, C. Millot, B. Maigret, and P. A. Kollman, J. Chem. Phys., 101, 7953 (1994). Molecular Dynamics Free Energy Simulations: Influence of the Truncation of Long Range Non-bonded Electrostatic Interactions on Free Energy Calculations of Polar Molecules.
76. A. Warshel, F. Sussman, and G. King, Biochemistry, 25, 8368 (1986). Free Energy of Changes in Solvated Proteins: Microscopic Calculations Using a Reversible Charging Process.
77. T. P. Straatsma and H. J. C. BerendsenJ. Chem. Phys., 89, 5876 (1988). Free Energy of Ionic Hydration.
78. W. F. van Gunsteren, in Modelling of Molecular Structures and Properties, Studies in Physical and Theoretical Chemistry, Vol. 71, J.-L. Rivail, Ed., Elsevier, Amsterdam, 1990, pp. 463-478. On Testing Theoretical Models by Comparison of Calculated with Experimental Data.
79. M. Born, Z. Physik, 1, 45 (1920). Volumen und Hydratationswärme der Ionen.
80. B. Jayaram, R. Fine, K. Sharp, and B. Honig, J. Chem. Phys., 93, 4320 (1989). Free Energy Calculations of Ion Hydration: An Analysis of the Born Model in Terms of Microscopic Simulations.
81. W. F. van Gunsteren and H. J. C. Berendsen, in Molecular Dynamics and Protein Structure, J. Hermans, Ed., Polycrystal Book Service, Western Springs, IL, 1985, pp. 18-22. Treatment of Long Range Forces in Molecular Dynamics.
82. A. C. Belch and M. Berkowitz, Chem. Phys. Lett., 113, 278 (1985). Molecular Dynamics Simulations of TIPS2 Water Restricted by a Spherical Hydrophobic Boundary.
83. H. J. C. Berendsen, in Proceedings of the Whistler Conference on Proteins, V. Renugopalakrishan, Ed., ESCOM, Leiden, 1990, pp. 385-392. Incomplete Equilibration: A Source of Error in Free Energy Calculations.
84. E. B. Smith and B. H. Wells, Mol. Phys., 53, 701 (1984). Estimating Errors in Molecular Simulation Calculations.
85. T. P. Straatsma, H. J. C. Berendsen, and A. J. Stam, Mol. Phys., 57, 89 (1986). Estimation of Statistical Errors in Molecular Simulation Calculations.
86. J. Kolafa, Mol. Phys., 59, 1035 (1986). Autocorrelations and Subseries Averages in Monte Carlo Simulations.
87. H. Flyvbjerg and H. G. Petersen, J. Chem. Phys., 91, 461 (1989). Error Estimates on Averages of Correlated Data.
88. R. H. Wood, W. C. F. Muhlbauer, and P. T. Thompson, J. Phys. Chem., 95, 6670 (1991). Systematic Errors in Free Energy Perturbation Calculations Due to a Finite Sample of Configuration Space: Sample-Size Hysteresis.
89. - with Ab Initio Potentials.
90. D. A. Pearlman and P. A. Kollman, J. Chem. Phys., 91, 7831 (1989). The Lag between Hamiltonians and the System Configuration in Free Energy Perturbation Calculations.
91. M. A. S. Saqi and J. M. Goodfellow, Protein Eng., 3, 419 (1990). Free Energy Changes Associated with Amino Acid Substitution in Proteins.
92. M. A. S. Saqi and J. M. Goodfellow, Mol. Simulation, 6, 185 (1991). Convergence Behavior in Free Energy Simulations.
93. M. H. Mazor and B. M. Pettitt, Mol. Simulation, 6, 1 (1991). Convergence of the Chemical Potential in Aqueous Solution.
94. J. Hermans, R. H. Yun, and A. G. Anderson, J. Comput. Chem., 13, 429 (1992). Precision of Free Energies Calculated by Molecular Dynamics Simulations of Peptides in Solution.
95. J. Hermans, J. Phys. Chem., 95, 9029 (1991). Simple Analysis of Noise and Hysteresis in (Slow Growth) Free Energy Simulations.
96. R. H. Wood, J. Phys. Chem., 95, 4838 (1991). Estimation of Errors in Free Energy Calculations Due to the Lag between the Hamiltonian and the System Configuration.
97. S. C. Harvey and M. Prabhakaran,J. Phys. Chem., 91, 4799 (1987). Umbrella Sampling: Avoiding Possible Artifacts and Statistical Biases.
98. C. F. Wong, J. Am. Chem. Soc., 113, 3208 (1991). Systematic Sensitivity Analysis in Free Energy Perturbation Calculations.
99. + in Water.
100. J. Åqvist, J. Phys. Chem., 94, 8021 (1990). Ion-Water Interaction Potentials Derived from Free Energy Perturbation Calculations.
101. J. Aqvist, J. Phys. Chem., 95, 4587 (1991). Free Energy Perturbation Study of Metal Ion Catalyzed Proton Transfer in Water.
102. R. M. Levy, M. Belhadj, and D. B. Kitchen, J. Chem. Phys., 95, 3627 (1991). Gaussian Fluctuation Formula for Electrostatic Free Energy Changes in Solution.
103. J. Wang and P. C. Jordan, J. Chem. Phys., 93, 2762 (1990). Application of the Thermodynamic Cycle Perturbation Method to Systems with Non-additive Potentials.
104. K. Ramnarayan, B. G. Rao, and U. C. Singh, J. Chem. Phys., 92, 7057 (1990). The Effect of Polarization Energy on the Free Energy Perturbation Calculations.
105. T. P. Straatsma and J. A. McCammon, Chem. Phys. Lett., 167, 252 (1990). Free Energy Thermodynamic Integrations in Molecular Dynamics Simulations Using a Non-iterative Method to Include Electronic Polarization.
106. T. P. Straatsma and J. A. McCammon, Mol. Simulation, 5, 181 (1990). Molecular Dynamics Simulations with Interaction Potentials Including Polarization. Development of a Noniterative Method and Application to Water.
107. T. P. Straatsma and J. A. McCammon, Chem. Phys. Lett., 177, 433 (1991). Free Energy Evaluations from Molecular Dynamics Simulations Using Force Fields Including Electronic Polarization.
108. B. G. Rao and U. C. Singh,J. Am. Chem. Soc., 112, 3803 (1990). A Free Energy Perturbation Study of Solvation in Methanol and Dimethyl Sulfoxide.
109. W. L. Jorgensen, J. M. Briggs, and M. L. Contreras, J. Phys. Chem., 94, 1683 (1990). Relative Partition Coefficients for Organic Solutes from Fluid Simulations.
110. Y. Tanaka, Y. Shiratori, and S. Nakagawa, Chem. Phys. Lett., 169, 513 (1990). Theoretical Studies of pKas for Organic Compounds in Aqueous Solution.
111. J. W. Essex, C. A. Reynolds, and W. G. Richards, J. Am. Chem. Soc., 114, 3634 (1992). Theoretical Determination of Partition Coefficients.
112. P. L. Cummins, K. Ramnarayan, U. C. Singh, and J. E. Gready,J. Am. Chem. Soc., 113, 8247 (1991). Molecular Dynamics Free Energy Perturbation Study on the Relative Affinities of Binding of Reduced and Oxidized NADP to Dihydrofolate Reductase.
113. B. G. Rao and U. C. Singh,J. Am. Chem. Soc., 113, 6735 (1991). Studies on the Binding of Pepstatin and Its Derivatives to Rhizopus Pepsin by Quantum Mechanics, Molecular Mechanics and Free Energy Perturbation.
114. B. G. Rao, R. F. Tilton, and U. C. Singh, J. Am. Chem. Soc., 114, 4447 (1992). Free Energy Perturbation Studies on Inhibitor Binding to HIV-1 Proteinase.
115. G. Wipff, P. K. Weiner, and P. A. Kollman, J. Am. Chem. Soc., 104, 3249 (1982). A Molecular Mechanics Study of 18-Crown-6 and Its Alkali Complexes an Analysis of Structural Flexibility, Ligand Specificity and the Macrocyclic Effect.
116. P. D. J. Grootenhuis and P. A. Kollman, J. Am. Chem. Soc., 111, 2152 (1989). Molecular Mechanics and Dynamics Studies of Crown Ether-Cation Interactions: Free Energy Calculations on the Cation Selectivity of Dibenzo-18-crown-6 and Dibenzo-30-crown-10.
117. P. D. J. Grootenhuis and P. A. Kollman, J. Am. Chem. Soc., 111, 4046 (1989). Crown Ether-Neutral Molecule Interactions Studied by Molecular Mechanics, Normal Mode Analysis, and Free Energy Perturbation Calculations; Near Quantitative Agreement between Theory and Experimental Binding Free Energies.
118. + and 18-Crown-6 in Methanol.
119. J. van Eerden, S. Harkema, and D. Feil, J. Phys. Chem., 92, 5076 (1988). Molecular Dynamics of 18-Crown-6 Complexes with Alkali Cations: Calculation of Relative Free Energies of Complexation.
120. + Complex in Water: a Molecular Dynamics Simulation.
121. T. P. Straatsma and J. A. McCammon, Annu. Rev. Phys. Chem., 43, 407 (1992). Computational Alchemy.
122. A. E. Torda and W. F. van Gunsteren, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, NY, 1992, Vol. 3, pp. 143-172. Molecular Modeling Using Nuclear Magnetic Resonance Data.
123. L. Troxler and G. Wipff, J. Am. Chem. Soc., 116, 1468 (1994). Conformation and Dynamics of 18-Crown-6, Cryptand 222 and Their Complexes in Acetonitrile Studied by Molecular Dynamics Simulations.
124. W. L. Jorgensen, Acc. Chem. Res., 22, 184 (1989). Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution.
125. W. L. Jorgensen and T. B. Nguyen, Proc. Natl. Acad. Sci. U.S.A., 90, 1194 (1993). Modeling the Complexation of Substituted Benzenes by a Cyclophane Host in Water.
126. P. R. Gerber, A. E. Mark, and W. F. van Gunsteren, J. Comput.-Aided Mol. Design, 7, 305 (1993). An Approximate but Efficient Method to Calculate Free Energy Trends by Computer Simulation: Application to Dihydrofolate Reductase - Inhibitor Complexes.
127. T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, and W. F. van Gunsteren, Chem. Phys. Lett., 222, 529 (1994). Avoiding Singularities and Numerical Instabilities in Free Energy Calculations Based on Molecular Simulations.
128. J. L. Scully and J. Hermans, Mol. Simulation, 11, 67 (1993). Multiple Time Steps: Limits on the Speedup of Molecular Dynamics Simulations of Aqueous Systems.
129. S. K. Schiferl and D. C. Wallace, J. Chem. Phys., 83, 5203 (1985). Statistical Errors in Molecular Dynamics Averages.
130. A. E. Mark, S. P. van Helden, P. E. Smith, L. H. M. Janssen, and W. F. van Gunsteren, J. Am. Chem. Soc., 116, 6293 (1994). Convergence Properties of Free Energy Calculations: α-Cyclodextrin Complexes as a Case Study.
131. R. A. Kendall, R. J. Harrison, R. J. Littlefield, and M. F. Guest, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1995, Vol. 6, pp. 209-316. High Performance Computing in Computational Chemistry: Methods and Machines.