References


Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids, Clarendon Press, Oxford Science Publications (1987).

Andersen, H. C. ``Molecular dynamics simulations at constant pressure and/or temperature'', J. Chem. Phys., 72, 2384 (1980).

Andersen, H. C. ``Rattle: A ``velocity'' version of the Shake algorithm for molecular dynamics calculations'', J. Comp. Physics, 52, 24-34 (1983).

Baccanari, D. P.; Daluge, S.; King, R. W. ``Inhibition of dihydrofolate reductase: Effect of reduced nicotinamide adenine dinucleotide phosphate on the selectivity and affinity of diaminobenzylpyrimidines'', Biochemistry, 21, 5068-5075 (1982).

Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. ``Molecular dynamics with coupling to an external bath'', J. Chem. Phys., 81, 3684-3690 (1984).

Born, M.; Oppenheimer, J. R. Ann. Physik, 84, 457 (1927).

Brooks, C. L., III; Montgomery; Pettitt, B.; Karplus, M. ``Structural and energetic effects of truncating long range interactions in ionic and polar fluids'', J. Chem. Phys., 83, 5897-5908 (1985).

Brown, D.; Clark, J. H. R. ``A comparison of constant energy, constant temperature, and constant pressure ensembles in molecular dynamics simulation of atomic liquids'', Molecular Physics, 51, 1243-1252 (1984).

Catlow, C. R. A.; Norgett, M. J. ``Lattice structure and stability of ionic materials'', personal communication (1976).

Dauber-Osguthorpe, P.; Roberts, V. A.; Osguthorpe, D. J.; Wolff, J.; Genest, M.; Hagler, A. T. ``Structure and energetics of ligand binding to proteins: E. coli dihydrofolate reductase-trimethoprim, a drug-receptor system'', Proteins: Structure, Function and Genetics, 4, 31-47 (1988).

Deem, M. W.; Newsam, J. M.; Sinha, S. K.. ``The h = 0 term in Coulomb sums by the Ewald transformation'', J. Phys. Chem., 94, 8356-8359 (1990).

Ding, H. Q.; Karasawa, N.; Goddard, W. A., III ``Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions'', J. Chem. Phys., 97, 4309 (1992).

Dinur, U.; Hagler, A. T. ``Approaches to empirical force fields'', in Review of Computational Chemistry, Vol. 2; Lipkwowitz, K. B.; Boyd, D. B. Eds.; VCH: New York; Chapter 4 (1991).

Ermer, O. ``Calculation of molecular properties using force fields. Applications in organic chemistry'', Structure and Bonding, 27, 161-211 (1976).

Fletcher, R. Practical Methods of Optimization, Vol. 1, Unconstrained Optimization, John Wiley & Sons: New York (1980).

Greengard, L.; Rokhlin, V. I. ``A fast algorithm for particle simulations'', J. Comp. Phys., 73, 325 (1987).

Ha, S. N.; Giammona, A.; Field, M.; Brady, J. W. ``A revised potential-energy surface for molecular mechanics studies of carbohydrates'', Carbohydrate Research, 180, 207-221 (1988).

Hagler, A. T. ``Theoretical simulation of conformation, energetics, and dynamics of peptides'', in Conformation in Biology & Drug Design, The Peptides; Meienhofer, J., Ed.; Academic Press, New York; 7, 213-299 (1985).

Hagler, A. T.; Dauber, P.; Lifson, S. ``Consistent force field studies of intermolecular forces in hydrogen bonded crystals. III. The C=OH-O hydrogen bond and the analysis of the energetics and packing of carboxylic acids'', J. Am. Chem. Soc., 101, 5131-5141 (1979b).

Hagler, A. T.; Ewig, C. S. ``On the use of quantum energy surfaces in the derivation of molecular force fields'', Comp. Phys. Comm., 84, 131-155 (1994).

Hagler, A. T.; Lifson, S.; Dauber, P. ``Consistent force field studies of intermolecular forces in hydrogen bonded crystals. II. A benchmark for the objective comparison of alternative force fields'', J. Am. Chem. Soc., 101, 5122-5130 (1979a).

Hagler, A. T.; Osguthorpe, D. J.; Dauber-Osguthorpe, P.; Hemple, J. C. ``Dynamics and conformational energetics of a peptide hormone: Vasopressin'', Science, 227, 1309-1315 (1985).

Hagler, A. T.; Stern, P. S.; Sharon, R.; Becker, J. M.; Naider, F. ``Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results'', J. Am. Chem. Soc., 101, 6842-6852 (1979c).

Hill, J. R.; Sauer, J. ``Molecular mechanics potential for silica and zeolite catalysts based on ab initio calculations. 1. Dense and microporous silica'', J. Phys. Chem., 98, 1238-1244 (1994).

Homans, S. W. ``A molecular mechanical force field for the conformational analysis of oligosaccharides: Comparison of theoretical and crystal structures of Man alpha1-3 Man beta1-4 GlcNAc'', Biochemistry, 29, 9110-9118 (1990).

Hoover, W. ``Canonical dynamics: Equilibrium phase-space distributions'', Phys. Rev., A31, 1695-1697 (1985).

Hwang, J. K.; Warshel, A. ``Semiquantitative calculations of catalytic free energies in genetically modified enzymes'', Biochemistry, 26, 2669-2673 (1987).

Hwang, M.-J.; Stockfisch, T. P.; Hagler, A. T. ``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. Amer. Chem. Soc., 116, 2515-2525 (1994).

Jorgensen, W. L.; Chandrasekhar, H.; Madura, J. D.; Impey, R. W.; Klein, M. L. J.Chem.Phys., 79, 926 (1983).

Karasawa, N.; Goddard, W. A., III ``Acceleration of convergence for lattice sums'', J. Phys. Chem., 93, 7320-7327 (1989).

Kirkwood, J. G. ``Statistical mechanics of fluid mixtures'', J. Chem. Phys., 3, 300-313 (1935).

Kitson, D. H.; Hagler, A. T. ``Theoretical studies of the structure and molecular dynamics of a peptide crystal'', Biochemistry, 27, 5246-5257 (1988).

Mackay, D. H. J.; Cross, A. J.; Hagler, A. T. ``The role of energy minimization in simulation strategies of biomolecular systems,'' In Prediction of Protein Structure and the Principles of Protein Conformation, G. Fasman, Ed.; Plenum Press, N.Y., 317-358 (1989).

Maple, J.; Dinur, U.; Hagler, A. T. ``Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces'', Proc. Nat. Acad. Sci. USA, 85, 5350-5354 (1988).

Maple, J. R.; Hwang, M.-J.; Stockfisch, T. P.; Dinur, U.; Waldman, M.; Ewig, C. S; Hagler, A. T. ``Derivation of Class II force fields. 1. Methodology and quantum force field for the alkyl functional group and alkane molecules'', J. Comput. Chem., 15, 162-182 (1994).

Maple, J. R.; Hwang, M.-J.; Stockfisch, T. P.; Hagler, A. T. ``Derivation of Class II force fields. 3. Characterization of a quantum force field for the alkanes'', Israel J. Chem.,34, 195-231 (1994).

Maple, J. R., Thacher, T. S., Dinur, U.; Hagler, A. T. ``Biosym force field research results in new techniques for the extraction of inter- and intramolecular forces'', Chemical Design Automation News, 5 (9), 5-10 (1990).

McQuarrie, Statistical Mechanics, Harper & Row, Chapter 3 (1976).

Mezei, M.; Beveridge, D. ``Free energy simulations'', Ann. N.Y. Acad. Sci., 482, 1-23 (1986).

Nosé, S. ``A molecular dynamics method for simulations in the canonical ensemble'', Molec. Phys., 52, 255-268 (1984a).

Nosé, S. ``A unified formulation of the constant temperature molecular dynamics methods'', J. Chem. Phys., 81, 511-519 (1984b).

Nosé, S. ``Constant temperature molecular dynamics methods'', Prog. Theoret. Phys. Supplement, 103, 1-46 (1991).

Ousterhout, J. K. Tcl and the Tk Toolkit; Addison-Wesley, Reading, (1994).

Parrinello, M.; Rahman, A. ``Polymorphic transitions in single crystals: A new molecular dynamics method'', J. Appl. Phys., 52, 7182-7190 (1981).

Poe, M.; Hoogstein, K.; Matthews, D. A. ``Proton magnetic resonance studies on E. coli dihydrofolate reductase'', J. Biol. Chem., 254, 8143-8152 (1979).

Press, W. H.: Flannery, B. P.; Teukolsky, S. A.; Vetterling, W. T. In Numerical Recipes, The Art of Scientific Computing; Cambridge University Press, Cambridge (1986).

Quirke, N.; Jacucci, G. ``Energy difference functions in Monte Carlo simulations: Application to (1) the calculation of free energy of liquid nitrogen. II. The calculation of fluctuation in Monte Carlo averages'', Mol. Phys., 45, 823-838 (1982).

Reidl, D., International Tables for Crystallography: A Space-Group Symmetry, Vol. A; Dordrecht, Holland (1983).

Roberts, V. A.; Dauber-Osguthorpe, P.; Osguthorpe, D. J.; Levin, E.; Hagler, A. T. ``A comparison of the binding of the ligand trimethoprim to bacterial and vertebrate dihydrofolate reductases'', Israel J. Chem., 27, 198-210 (1986).

Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. ``Numerical Integration of the Carte sian equations of motion of a system with constraints: Molecular dynamics of n-alkanes'', J. Comp. Phys., 23, 327-341 (1977). Schmidt, K. E.; Lee, M. A. ``Implementing the fast multipole method in three dimensions'', J. Stat. Phys., 63, 1223 (1991).

Singh, U. C; Brown, F. K.; Bash, P. A.; Kollman, P. A. ``An approach to the application of free energy perturbation methods using molecular dynamics: Applications to the transformations of methanol to ethane, oxonium to ammonium, glycine to alanine, and alanine to phenylalanine in aqueous solution and to H3O+(H2O)3 NH4+(H2O)3 in the gas phase'', J. Am. Chem. Soc., 109, 1607-1614 (1987).

Straatsma, T. P.; Berendsen, H. J. C.; Postma, J. P. M. ``Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water'', J. Chem. Phys., 85, 6720-6727 (1986).

Struthers, R. S.; Rivier, J.; Hagler, A. T. ``Design of peptide analogs: Theoretical simulation of conformation, energetics, and dynamics'', in Conformationally Directed Drug Design: Peptides and Nucleic Acids as Templates or Targets, J. A. Vida and M. Gordon, Eds., American Chemical Society, Washington, 239-261 (1984).

Sun, H.; Mumby, S. J.; Maple, J. R.; Hagler, A. T. ``An ab initio CFF93 all-atom force field for polycarbonates'', J. Amer. Chem. Soc., 116, 2978-2987 (1994).

Tembe, B. L.; McCammon, J. A. ``Ligand-receptor interactions'', Comput. Chem., 8, 281-283 (1984).

Tosi, M. P., Solid State Physics, 16, 107 (1964).

Verlet, L. ``Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules'', Phys. Rev., 159, 98-103 (1967).

Waldman, M.; Hagler, A. T. ``New combining rules for rare gas van der Waals parameters'', J. Comput. Chem., 14, 1077-1084 (1993).

Warshel, A.; Sussman, F.; King, G. ``Free energy of charges in solvated proteins: Microscopic calculations using a reversible charging process'', Biochemistry, 25, 8368-8372 (1986).

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

Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. ``An all atom forcefield for simulations of proteins and nucleic acid'', J. Comp. Chem., 7, 230-252 (1986).

Wiberg, K. B.; Murcko, M. A., J. Am. Chem. Soc., 111, 4821 (1989).

Wilson, E. B.; Decius, J. C.; Cross, P. C. Molecular Vibrations, Dover, New York (1980).


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