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Empirical Classical Force Fields for Molecular Systems

  • Conference paper
Potential Energy Surfaces

Part of the book series: Lecture Notes in Chemistry ((LNC,volume 71))

Abstract

With the continuing increase of the power of computers, the past decades have seen a rapid increase in the number, performance and accuracy of theoretical computational methods in chemistry (van Gunsteren et al., 1989 ff, Lipkowitz & Boyd, 1990ff). One can distinguish three major classes of methods for the theoretical study of molecular properties, listed in order of decreasing computational expenses: (i) ab initio molecular-orbital methods (Hehre et al., 1986), (ii) semi-empirical molecular-orbital methods (Zerner, 1991), and (iii) empirical classical force-field methods. Since the available computing resources are most often the true limiting factor to numerical calculations, it has become clear that there is no universal method able to solve all possible problems, but that one should rather select the method that is the most suitable to a problem of interest. The properties of the observable (s) and system under consideration that will, together with the available computing power, largely determine which type of method can be used are (van Gunsteren & Berendsen, 1990): (i) the required system size, (ii) the required volume of conformational space that has to be searched or sampled (in terms of dynamics: the required time-scale), (iii) the required resolution in terms of particles (determined by the smallest entity, subatomic particle, atom, or group of atoms, treated explicitly in the model), and (iv) the required energetical accuracy of the interaction function. These requirements may be incompatible, in which case the observable cannot be computed adequately with the currently available computer resources (van Gunsteren et al., 1995b). When requirements (i) and (ii) are in conflict with requirement (iii), this conflict may be resolved by the design of hierarchical or hybrid models, where only the relevant degrees of freedom are treated with a more expensive, higher resolution method. This is often done, for example, in the study of acid- or base-catalysed, organic or enzymatic reactions in the bulk phase (Warshel, 1991, Field, 1993, Whitnell & Wilson, 1993, Liu et al., 1996a).

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References

  • Allen, M. P. & Tildesley, D. J. (1987). Computer simulation of liquids, Oxford University Press, Oxford, pp 1–385

    Google Scholar 

  • Allinger, N. L. (1977). Conformational analysis. 130. MM2. A hydrocarbon force field utilizing VI and V2 torsional terms. J. Am. Chem. Soc. 99, 8127–8134

    CAS  Google Scholar 

  • Allinger, N. L., Yuh, Y. H. & Lii, J. -H. (1989). Molecular mechanics. The MM3 force field for hydrocarbons. 1. J. Am. Chem. Soc. Ill, 8551–8566

    Google Scholar 

  • Angyän, J. G. (1992). Common theoretical framework for quantum chemical solvent effect theories. J. Math. Phys. 10, 93–137

    Google Scholar 

  • Barker, J. A. & Watts, R. O. (1973). Monte Carlo studies of the dielectric properties of water-like models. Mol. Phys. 26, 789–792

    CAS  Google Scholar 

  • Barker, J. A. (1994). Reaction field, screening, and long-range interactions in simulations of ionic and dipolar systems. Mol. Phys. 83, 1057–1064

    CAS  Google Scholar 

  • Beglov, D. & Roux, B. (1994). Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations. J. Chem. Phys. 100, 9050–9063

    CAS  Google Scholar 

  • Berendsen, H. J. C (1993). Electrostatic interactions. In: Computer simulation of biomolecular systems, theoretical and experimental applications, Vol. II, van Gunsteren, W. F., Weiner, P. K. & Wilkinson, A. J., Eds., ESCOM Science Publishers, B. V., Leiden, The Netherlands, pp 161–181

    Google Scholar 

  • Beutler, T. C., Mark, A. E., van Schaik, R. C., Gerber, P. R. k van Gunsteren, W. F. (1994). Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem. Phys. Lett. 222, 529–539

    CAS  Google Scholar 

  • Beutler, T. C. k van Gunsteren, W. F. (1994). Molecular dynamics free energy calculation in four dimensions. J. Chem. Phys. 101, 1417–1422

    CAS  Google Scholar 

  • Binder, K. (1992). Topics in applied physics, Vol. 71: The Monte Carlo method in condensed matter physics, Springer-Verlag, Berlin

    Google Scholar 

  • Bowen, J. P. & Allinger, N. L. (1991). Molecular mechanics: The art and science of parametrization. In: Reviews in computational chemistry, Vol. II, Lipkowitz, K. B. k Boyd, D. B., Eds., VCH Publishers Inc., New York, pp 81–97

    Google Scholar 

  • Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. k Karplus, M. (1983). CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187–217

    CAS  Google Scholar 

  • Brooks III, C. L., Pettitt, B. M. k Karplus, M. (1985). Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids. J. Chem. Phys. 83, 5897–5908

    CAS  Google Scholar 

  • Brooks III, C. L. (1987). The influence of long-range force truncation on the thermodynamics of aqueous ionic solutions. J. Chem. Phys. 86, 5156–5162

    CAS  Google Scholar 

  • Brooks III, C. L., Karplus, M., Pettitt, B. M. (1988). Proteins: A theoretical perspective of dynamics, structure and thermodynamics, Wiley series on advances in chemical physics, Vol LXXI, Prigogine, I. & Rice, S., Eds., John Wiley & Sons, New York, pp 1–259

    Google Scholar 

  • Brown, F. B. & Truhlar, D. G. (1985). Dissociation potential for breaking a C-H bond in methane. Chem. Phys. Lett. 113, 441–446

    CAS  Google Scholar 

  • Chipot, C., Millot, C., Maigret, B. & Kollman, P. A. (1994a). Molecular dynamics free energy simulations: Influence of the truncation of long-range nonbonded electrostatic interactions on the free energy calculations of polar molecules. J. Chem. Phys. 101, 7953–7962

    CAS  Google Scholar 

  • Chipot, C., Millot, C., Maigret, B. & Kollman, P. A. (1994b). Molecular dynamics free energy perturbation calculations: Influence of nonbonded parameters on the free energy of hydration of charged and neutral species. J. Phys. Chem. 98, 11362–11372

    CAS  Google Scholar 

  • Clark, M., Cramer III, R. D. & van Opdenbosch, N. (1989). Validation of the general purpose Tripos 5. 2 force field. J. Comput. Chem. 10, 982–1012

    CAS  Google Scholar 

  • Cramer, C. J. & Truhlar, D. G. (1992). An SCF solvation model for the hydrophobic effect and absolute free energies of aqueous solvation. Science 256, 213–217

    CAS  Google Scholar 

  • Cramer, C. J. & Truhlar, D. G. (1994). Continuum solvation models: Classical and quantum mechanical implementations. In: Reviews in computational chemistry, Vol. VI, Lipkowitz, K. B. & Boyd, D. B., Eds., VCH Publishers Inc., New York, pp 1–70

    Google Scholar 

  • Curtiss, L. A. & Jürgens, R. (1990). Nonadditivity of interaction in hydrated Cu+ and Cu2+ clusters. J. Am. Chem. Soc. 94, 5509–5513

    CAS  Google Scholar 

  • Daura, X., Hünenberger, P. H., Mark, A. E., Querol, E., Aviles, F. X. & van Gunsteren, W. F. (1996). Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment, and importance of adequate treatment of electrostatic and internal interaction. J. Am. Chem. Soc. 118, 6285–6294

    CAS  Google Scholar 

  • Davis, M. E. & McCammon, J. A. (1990). Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90, 509–521

    CAS  Google Scholar 

  • Dillen, J. L. M. (1995a). An empirical force field. I. Alkanes. J. Comput. Chem. 16, 565–609

    Google Scholar 

  • Dillen, J. L. M. (1995b). An empirical force field. II. Crystalline alkanes. J. Comput. Chem. 16, 610–615

    CAS  Google Scholar 

  • Dinur, U. & Hagler, A. T. (1991). New approaches to empirical force fields. In: Reviews in computational chemistry, Vol. II, Lipkowitz, K. B. & Boyd, D. B., Eds., VCH Publishers Inc., New York, pp 99–164

    Google Scholar 

  • Dinur, U. & Hagler, T. A. (1994). On the functional representation of bond energy functions. J. Comput. Chem. 9, 919–924

    Google Scholar 

  • Elrod, M. J. & Saykally, R. J. (1994). Many-body effects in intermolecular forces. Chem. Rev. 94, 1975–1997

    CAS  Google Scholar 

  • Engelsen, S. B., Fabricius, J. & Rasmussen, K. (1995a). The consistent force field. 1. Methods and strategies for optimization of empirical potential energy functions. Acta Chem. Scand. 48, 548–552

    Google Scholar 

  • Engelsen, S. B., Fabricius, J. & Rasmussen, K. (1995b). The consistent force field. 2. An optimized set of potential energy functions for the alkanes. Acta Chem. Scand. 48, 553–565

    Google Scholar 

  • Ermler, W. C. & Hsieh, H. C. (1990). Analytical representation and vibrational-rotational analysis of ab initio potential energy and property surfaces, In: Advances in molecular electronic structure theory, Vol. 1, Calculation and characterization of molecular potential energy surfaces, Dunning Jr., T. H., Ed., JAI Press Inc., London, pp 1–44

    Google Scholar 

  • Essex, J. W. & Jorgensen, W. L. (1995). An empirical boundary potential for water droplet simulations. J. Comput. Chem. 16, 951–972

    CAS  Google Scholar 

  • Fincham, D. (1994). Optimisation of the Ewald sum for large systems. Mol. Sim. 13, 1–9

    CAS  Google Scholar 

  • Fraternali, F. & van Gunsteren, W. F. (1996). An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. J. Mol. Biol. 256, 939

    CAS  Google Scholar 

  • Frenkel, D. (1993). Monte Carlo simulations: A primer. In: Computer simulation of biomolecular systems, theoretical and experimental applications, Vol. II, van Gunsteren, W. F., Weiner, P. K. & Wilkinson, A. J., Eds., ESCOM Science Publishers, B. V., Leiden, The Netherlands, pp 37–66

    Google Scholar 

  • Field, M. J. (1993). The simulation of chemical reactions. In: Computer simulation of biomolecular systems, theoretical and experimental applications, Vol. II, van Gunsteren, W. F., Weiner, P. K. & Wilkinson, A. J., Eds., ESCOM Science Publishers, B. V., Leiden, The Netherlands, pp 82–123

    Google Scholar 

  • Figueirido, F., Del Buono, G. S. & Levy, R. M. (1995). On finite-size effects in computer simulations using the Ewald potential. J. Chem. Phys. 103, 6133–6142

    CAS  Google Scholar 

  • Gelin, B. R. (1993). Testing and comparison of empirical force fields: Techniques and problems. In: Computer simulation of biomolecular systems, theoretical and experimental applications, Vol. II, van Gunsteren, W. F., Weiner, P. K. & Wilkinson, A. J., Eds., ESCOM Science Publishers, B. V., Leiden, The Netherlands, pp 127–146

    Google Scholar 

  • Gerber, P. R. (1992). Peptide mechanics: a force-field for peptides and proteins working with entire residues as smallest units. Biopolymers 32, 1003–1017

    CAS  Google Scholar 

  • Gerber, P. R. & Miiller, K. (1995). MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry. J. Comput. Aided Mol. Design 9, 251–268

    CAS  Google Scholar 

  • Hagler, A. T., Lifson, S. & Dauber, P. (1979a). Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 2. A benchmark for the objective comparison of alternative force fields. J. Am. Chem. Soc. 101, 5122–5130

    CAS  Google Scholar 

  • Hagler, A. T., Lifson, S. & Dauber, P. (1979b). Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 3. The C=0 H-0 hydrogen bond and the analysis of the energetics and packing of carboxylic acids. J. Am. Chem. Soc. 101, 5131–5141

    CAS  Google Scholar 

  • Hagler, A. T., Stern, P. S., Sharon, R., Becker, J. M. & Naider, F. (1979c). Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results. J. Am. Chem. Soc. 101, 6842–6852

    CAS  Google Scholar 

  • Hagler, A. T. & Ewig, C. S. (1994). On the use of quantum energy surfaces in the derivation of molecular force fields. Comp. Phys. Commun. 84, 131–155

    CAS  Google Scholar 

  • Halgren, T. A. (1990). Maximally diagonal force constants in dependent angle-bending coordinates. 2. Implications for the design of empirical force-fields. J. Am. Chem. Soc. 112, 4710–4723

    CAS  Google Scholar 

  • Halgren, T. A. (1992). Representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters. J. Am. Chem. Soc. 114, 7827–7843

    CAS  Google Scholar 

  • Hart, J. R. & Rappe, A. K. (1992a). Van der Waals functional forms for molecular simulations. J. Chem. Phys. 97, 1109–1115

    CAS  Google Scholar 

  • Hart, J. R. & Rappe, A. K. (1992b). Reply to comment on: van der Waals functional forms for molecular simulations. J. Chem. Phys. 98, 2492

    Google Scholar 

  • Harvey, S. C. (1989). Treatment of electrostatic effects in macromolecular modeling. Proteins: Struct. Fund. Genet. 5, 78–92

    CAS  Google Scholar 

  • Hehre, W. J., Radom, L., Schleyer, P. v. R & Pople, J. A. (1986). Ab initio molecular orbital theory, John Wiley & Sons, New York, pp 1–548

    Google Scholar 

  • Huber, T., Torda, A. E. & van Gunsteren, W. F. (1994). Local elevation: A method for improving the searching properties of molecular dynamics simulation. J. Comput.-Aided Mol. Design 8, 695–708

    CAS  Google Scholar 

  • Hummer, G., Soumpasis, D. M. & Neumann, M. (1992). Pair correlations in an NaCl-SPC water model. Simulations versus extended RISM computations. Mol. Phys. 77, 769–785

    CAS  Google Scholar 

  • Hiinenberger, P. H., Mark, A. E. & van Gunsteren, W. F. (1995a). Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study. Proteins: Struct. Funct. Genet. 21, 196–213

    Google Scholar 

  • Hiinenberger, P. H., Mark, A. E. & van Gunsteren, W. F. (1995b). Fluctuation and crosscorrelation analysis of protein motions observed in nanosecond molecular dynamics simulations. J. Mol. Biol. 252, 492–503

    Google Scholar 

  • Hwang, M. J., Stockfisch, T. P. & Hagler, A. T. (1994). Derivation of class II force-fields. 2. Derivation and characterization of a class II force field, CFF93, for the alkyl functional group and alkane molecules. J. Am. Chem. Soc. 116, 2515–2525

    CAS  Google Scholar 

  • Jones, D. T. (1994). De novo protein design using pairwise potentials and genetic algorithm. Prot. Sci. 3, 567–574

    CAS  Google Scholar 

  • Jorgensen, W. L. & Tirado-Rives, J. (1988). The OPLS potential fonctions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110, 1657–1666

    CAS  Google Scholar 

  • Keith, T. A. & Frisch, M. J. (1994). Inclusion of explicit solvent molecules in a selfconsistent-reaction field model of solvation, In: Modeling the hydrogen bond, Smith, D. A., Ed., American Chemical Society, Washington DC, pp 22–35

    Google Scholar 

  • Kestin, J., Knierim, K., Mason, E. A., Najafi, B., Ro, S. T. & Waldman, M. (1984). Equilibrium and transport properties of the noble gases and their mixtures at low density. J. Phys. Chem. Ref. Data 13, 229–303

    CAS  Google Scholar 

  • King, G. & Warshel, A. (1989). A surface constrained all-atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91, 3647–3661

    CAS  Google Scholar 

  • Levitt, M. (1974). Energy refinement of hen egg-white lysozyme. J. Mol. Biol. 82, 393–420

    CAS  Google Scholar 

  • Levitt, M. (1983a). Molecular dynamics of native proteins. I. Computer simulation of trajectories. J. Mol. Biol. 168, 595–620

    CAS  Google Scholar 

  • Levitt, M. (1983b). Molecular dynamics of native protein. II. Analysis and nature of motion. J. Mol Biol. 168, 621–657

    CAS  Google Scholar 

  • Levitt, M., Hirshberg, M., Sharon, R. & Daggett, V. (1995). Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput. Phys. Commun. 91, 215–231

    CAS  Google Scholar 

  • Lifson, S. & Warshel, A. (1968). Consistent force field calculations of conformations, vibrational spectra, and enthalpies of cycloalkane and n-alkane molecules. J. Chem. Phys. 49, 5116–5129

    CAS  Google Scholar 

  • Lifson, S., Hagler, A. T. & Dauber, P. (1979). Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 1. Carboxylic acids, amides, and the C=0-H hydrogen bonds. J. Am. Chem. Soc. 101, 5111–5121

    CAS  Google Scholar 

  • Lifson, S. & Stern, P. S. (1982). Born-Oppenheimer energy surfaces of similar molecules: Interrelations between bond lengths, bond angles, and frequencies of normal vibrations in alkanes. J. Chem. Phys. 77, 4542–4550

    CAS  Google Scholar 

  • Lii, J. -H. & Allinger, N. L. (1989a). Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics. J. Am. Chem. Soc. III, 8566–8575

    Google Scholar 

  • Lii, J. -H. & Allinger, N. L. (1989b). Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals potentials and crystal data for aliphatic and aromatic hydrocarbons. J. Am. Chem. Soc. III, 8576–8582

    Google Scholar 

  • Lipkowitz, K. B. & Boyd, D. B. (1990ff). Reviews in computational chemistry, Vol. I–VII, VCH Publishers Inc., New York

    Google Scholar 

  • Liu, H., Miiller-Plathe, F. & van Gunsteren, W. F. (1994). A molecular dynamics simulation study with a combined quantum mechanical and molecular mechanical potential energy function: Solvation effects on the conformational equilibrium of dimethoxyethane. J. Chem. Phys. 102, 1722–1730

    Google Scholar 

  • Liu, H., Miiller-Plathe, F. & van Gunsteren, W. F. (1996a). A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV-protease. J. Mol. Biol. 261, 454

    CAS  Google Scholar 

  • Liu, H., Miiller-Plathe, F. & van Gunsteren, W. F. (1996b). Molecular dynamics with a quantum-chemical potential: Solvent effect on an SN2 reaction at nitrogen. Chem. Eur. J. 2, 191

    CAS  Google Scholar 

  • Loncharich, R. J. & Brooks, B. R. (1989). The effects of truncating long-range forces on protein dynamics. Proteins: Struct. Funct. Genet. 6, 32–45

    CAS  Google Scholar 

  • Luty, B. A., Tironi, I. G. & van Gunsteren, W. F. (1995). Lattice-sum methods for calculating electrostatic interactions in molecular simulations. J. Chem. Phys. 103, 3014–3021

    CAS  Google Scholar 

  • Luty, B. A. & van Gunsteren, W. F. (1996). Calculating electrostatic interactions using Particle-Particle-Particle-Mesh method with non-periodic long-range interactions. J. Phys. Chem. 100, 2581

    CAS  Google Scholar 

  • MacKerell Jr., A. D., Wiorkiewicy-Kuczera, J. & Karplus, M. (1995). An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117, 11946–11975

    CAS  Google Scholar 

  • Madura, J. D. & Pettitt, B. M. (1988). Effects of truncating long-range interactions in aqueous ionic solution simulations. J. Chem. Phys. 150, 105–108

    CAS  Google Scholar 

  • Maple, J. R., Dinur, U. & Hagler, A. T. (1988). Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces. Proc. Natl. Acad. Sci. USA 85, 5350–5354

    CAS  Google Scholar 

  • Maple, J. R., Hwang, M. -J., Stockfisch, T. P., Dinur, U., Waldman, M., Ewig, C. S. & Hagler, A. T. (1994a). Derivation of class II force-fields. I. Methodology and quantum force-field for the alkyl functional group and alkane molecules. J. Comput. Chem. 15, 162–182

    CAS  Google Scholar 

  • Maple, J. R., Hwang, M. -J., Stockfisch & Hagler, A. T. (1994b). Derivation of class II force fields. III. Characterization of a quantum force field for alkanes. Isr. J. Chem. 34, 195–231

    CAS  Google Scholar 

  • Mayo, S. L., Olafson, B. D. & Goddard III, W. A. (1990). DREIDING: A generic force-field for molecular simulations. J. Phys. Chem. 94, 8897–8909

    CAS  Google Scholar 

  • McCammon, J. A. & Harvey, S. C. (1987). Dynamics of proteins and nucleic acids, Cambridge University Press, Cambridge

    Google Scholar 

  • Momany, F. A. k Rone, R. (1992). Validation of the general purpose QUANTA 3. 2/CHARMm force field. J. Comput. Chem. 13, 888–900

    CAS  Google Scholar 

  • Miiller-Plathe, F. & van Gunsteren, W. F. (1994). Can simple quantum-chemical continuum models explain the gauche effect in poly (ethylene oxyde)? Macromolecules 27, 6040–604

    Google Scholar 

  • Nemethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S. & Scheraga, H. A. (1992). Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interaction for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96, 6472–6484

    CAS  Google Scholar 

  • Neumann, M. (1983). Dipole moment fluctuation formulas in computer simulations of polar systems. Mol. Phys. 50, 841–858

    CAS  Google Scholar 

  • Neumann, M., Steinhauser, O. & Pawley, G. S. (1984). Consistent calculation of the static and frequency-dependent dielectric constant in computer simulations. Mol. Phys. 52, 97–113

    CAS  Google Scholar 

  • Nilsson, L. & Karplus, M. (1986). Empirical energy functions for energy minimization and dynamics of nucleic acids. J. Comput. Chem. 7, 591–616

    CAS  Google Scholar 

  • Oie, T., Maggiora, G. M., Christoffersen, R. E. & Duchamp, D. J. (1981). Development of a flexible intra-and intermolecular empirical potential function for large molecular systems. Int. J. Quant. Chem. Quant. Biol. Symp. 8, 1–47

    CAS  Google Scholar 

  • Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham III, T. E., DeBolt, S., Ferguson, D., Seibel, G. k Kollman, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91, 1–41

    CAS  Google Scholar 

  • Pettitt, B. M. & Karplus, M. (1985). Role of electrostatics in the structure, energy, and dynamics of biomolecules: A model study of N-methylalanyl-acetamide. J. Am. Chem. Soc. 107, 1166–1173

    CAS  Google Scholar 

  • Prevost, M., van Belle, D., Lippens, G. & Wodak, S. (1990). Computer simulations of liquid water: treatment of long-range interactions. Mol. Phys. 71, 587–603

    CAS  Google Scholar 

  • Rappe, A. K., Casewit, C. J., Colwell, K. S., Goddard III, W. A. & Skiff, W. M. (1992). UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 114, 10024–10035

    CAS  Google Scholar 

  • Rüssel, S. T. & Warshel, A. (1985). Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor. J. Mol. Biol. 185, 389–404

    Google Scholar 

  • Schreiber, H. & Steinhauser, O. (1992a). Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. J. Mol. Biol. 228, 909–923

    CAS  Google Scholar 

  • Schreiber, H. & Steinhauser, O. (1992b). Molecular dynamics studies of solvated polypeptides: Why the cut-off scheme does not work. Chem. Phys. 168, 75–89

    CAS  Google Scholar 

  • Schreiber, H. & Steinhauser, O. (1992c). Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry 31, 5856–5860

    CAS  Google Scholar 

  • Smith, J. C. & Karplus, M. (1992). Empirical force field study of geometries and conformational transitions of some organic molecules. J. Am. Chem. Soc. 114, 801–812

    CAS  Google Scholar 

  • Smith, P. E. & van Gunsteren, W. F. (1993). Methods for the evaluation of long range electrostatic forces in computer simulations of molecular systems. In: Computer simulation of biomolecular systems, theoretical and experimental applications, Vol. II, van Gunsteren, W. F., Weiner, P. K. & Wilkinson, A. J., Eds., ESCOM Science Publishers, B. V., Leiden, The Netherlands, pp 182–212

    Google Scholar 

  • Smith, P. E. & Pettitt, B. M. (1995). Efficient Ewald electrostatic calculations for large systems. Comput. Phys. Commun. 91, 339–344

    CAS  Google Scholar 

  • Smith, P. E. & van Gunsteren, W. F. (1995). Reaction field effects on the simulated properties of liquid water. Mol. Sim. 15, 233–245

    CAS  Google Scholar 

  • Steinbach, P. J. & Brooks, B. R. (1994). New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem. 15, 667–683

    CAS  Google Scholar 

  • Tironi, I. G., Sperb, R., Smith, P. E. & van Gunsteren, W. F. (1995). A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102, 5451–5459

    CAS  Google Scholar 

  • Tomasi, J. & Persico, M. (1994). Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent. Chem. Rev. 94, 2027–2094

    CAS  Google Scholar 

  • Ulrich, P., Scott, W., van Gunsteren, W. F. & Torda. A. E (1997). Protein structure prediction force fields: parametrization with quasinewtonian dynamics. Proteins: Struct. Funct. Genet. 27, 367–384

    CAS  Google Scholar 

  • van Gunsteren, W. F. & Karplus, M. (1982). Effect of constraints on the dynamics of macromolecules. Macromolecules 15, 1528–1544

    Google Scholar 

  • van Gunsteren, W. F. & Berendsen, H. J. C (1987). Groningen molecular simulation (GROMOS) library manual, Biomos, Nijenborgh 4, Groningen, The Netherlands van Gunsteren, W. F., Weiner, P. K. & Wilkinson, A. J. (1989ff). Computer simulation of biomolecular systems, theoretical and experimental applications, Vol. I–II, ESCOM Science Publishers, B. V., Leiden, The Netherlands

    Google Scholar 

  • van Gunsteren, W. F. & Berendsen, H. J. C (1990). Computer simulation of molecular dynamics: Methodology, applications and perspectives in chemistry. Angew. Chem. Int. Ed. Engl. 29, 992–1023

    Google Scholar 

  • van Gunsteren, W. F. & Mark, A. E. (1992). On the interpretation of biochemical data by molecular dynamics computer simulation. Eur. J. Biochem. 204, 947–961

    Google Scholar 

  • van Gunsteren, W. F. (1993). Molecular dynamics and stochastic dynamics simulation: A primer. In: Computer simulation of biomolecular systems, theoretical and experimental applications, Vol. II, van Gunsteren, W. F., Weiner, P. K. & Wilkinson, A. J., Eds., ESCOM Science Publishers, B. V., Leiden, The Netherlands, pp 3–36

    Google Scholar 

  • van Gunsteren, W. F., Luque, F. J., Timms, D. & Torda, A. E. (1994). Molecular mechanics in biology: From structure to function, taking account of solvation. Annu. Rev. Biophys. Biomol. Struct. 23, 847–863

    Google Scholar 

  • van Gunsteren, W. F., Huber, T. & Torda, A. E. (1995a). Biomolecular modelling: overview of types of methods to search and sample conformational space. European Conference on Computational Chemistry (E. C. C. C. 1), American Institute of Physics Conf. Proc. 330, 253–268

    Google Scholar 

  • van Gunsteren, W. F., Hunenberger, P. H., Mark, A. E., Smith, P. E. & Tironi, I. G. (1995b). Computer simulation of protein motion. Chem. Phys. Commun. 91, 305–319

    Google Scholar 

  • van Schaik, R. C., Berendsen, H. J. C. Torda, A. E. & van Gunsteren, W. F. (1993). A structure refinement method based on molecular dynamics in four spatial dimensions. J. Mol. Biol. 234, 751–762

    Google Scholar 

  • Vedani, A. (1988). YETI: An interactive molecular mechanics program for small-molecule protein complexes. J. Comput. Chem. 9, 269–280

    CAS  Google Scholar 

  • Waldman, M. & Hagler, A. T. (1993). New combining rules for rare gas van der Waals parameters. J. Comput. Chem. 14, 1077–1084

    CAS  Google Scholar 

  • Wang, L. & Hermans, J. (1995). Reaction field molecular dynamics simulation with Friedman’s image charge method. J. Phys. Chem. 99, 12001–12007

    CAS  Google Scholar 

  • Warshel, A. & Lifson, S. (1970). Consistent force field calculations. II. Crystal structures, sublimation energies, molecular and lattice vibrations, molecular conformations, and enthalpies of alkanes. J. Chem. Phys. 53, 582–594

    CAS  Google Scholar 

  • Warshel, A. (1991). Computer modeling of chemical reactions in enzymes and solutions, Wiley-Interscience, John Wiley & Sons, Inc., New York, pp 1–236

    Google Scholar 

  • Weiner, P. K. & Kollman, P. A. (1981). AMBER: assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comput. Chem. 2, 287–303

    CAS  Google Scholar 

  • Weiner, S. J., Kollman, Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta Jr., S. & Weiner, P. (1984). A new force field for molecular mechanical simulations of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765–784

    Google Scholar 

  • Weiner, S. J., Kollman, P. A., Nguyen, D. T. & Case, D. A. (1986). An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7, 230–252

    CAS  Google Scholar 

  • Whitnell, R. M. & Wilson, K. R. (1993). Computational molecular dynamics of chemical reactions in solution. In: Reviews in computational chemistry, Vol. IV, Lipkowitz, K. B. & Boyd, D. B., Eds., VCH Publishers Inc., New York, pp 67–148

    Google Scholar 

  • Wood, R. H. (1995). Continuum electrostatics in a computational universe with finite cutoff radii and periodic boundary conditions: Correction to computed free energies of ionic solvation. J. Chem. Phys. 103, 6177–6187

    CAS  Google Scholar 

  • Yun-Yu, S., Lu, W. & van Gunsteren, W. F. (1988). On the approximation of solvent effects on the conformation and dynamics of cyclosporin A by stochastics dynamics simulation techniques. Mol. Sim. 1, 369–383

    Google Scholar 

  • Zavitsas, A. A. & Beckwith A. L. J (1989). New potential energy function for bond extensions. J. Phys. Chem. 93, 5419–5426

    CAS  Google Scholar 

  • Zerner, M. C. (1991). Semiempirical molecular orbital methods. In: Reviews in computational chemistry, Vol. II, Lipkowitz, K. B., Boyd, D. B., Eds., VCH Publishers Inc., New York, pp 313–365

    Google Scholar 

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Authors and Affiliations

  1. Dept. of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093-0365, USA

    Philippe H. Hünenberger

  2. Physical Chemistry Institute, ETH Zentrum, CAB, CH-8092, Zürich, Switzerland

    Wilfred F. van Gunsteren

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  1. Philippe H. Hünenberger
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  2. Wilfred F. van Gunsteren
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  1. Institute of Theoretical Chemistry, Karl-Franzens-Universität Graz, Strassoldogasse 10, A-8010, Graz, Austria

    Alexander F. Sax

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© 1999 Springer-Verlag Berlin Heidelberg

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Hünenberger, P.H., van Gunsteren, W.F. (1999). Empirical Classical Force Fields for Molecular Systems. In: Sax, A.F. (eds) Potential Energy Surfaces. Lecture Notes in Chemistry, vol 71. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-46879-7_4

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  • DOI: https://doi.org/10.1007/978-3-642-46879-7_4

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