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Index
- 1
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M. P. Allen and D. J. Tildesley.
Computer Simulation of Liquids.
Oxford University Press, New York, 1987.
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A. Altis, P. H. Nguyen, R. Hegger, and G. Stock.
Dihedral angle principal component analysis of molecular dynamics
simulations.
J. Chem. Phys., 126(24):244111, 2007.
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P. H. Axelsen and D. Li.
Improved convergence in dual-topology free energy calculations
through use of harmonic restraints.
J. Comput. Chem., 19:1278-1283, 1998.
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A. Barducci, G. Bussi, and M. Parrinello.
Well-tempered metadynamics: A smoothly converging and tunable
free-energy method.
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C. H. Bennett.
Efficient estimation of free energy differences with monte carlo
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The protein data bank: A computer-based archival file for
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The role of bonded terms in free energy simulations: I. theoretical
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D. Branduardi, F. L. Gervasio, and M. Parrinello.
From a to b in free energy space.
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Free energy calculations. Theory and applications in chemistry
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G. Ciccotti, R. Kapral, and E. Vanden-Eijnden.
Blue moon sampling, vectorial reaction coordinates, and unbiased
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Multiple-walker strategies for free-energy calculations in namd:
Shared adaptive biasing force and walker selection rules.
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E. A. Coutsias, C. Seok, and K. A. Dill.
Using quaternions to calculate RMSD.
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Adaptive biasing force method for scalar and vector free energy
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W. K. den Otter.
Thermodynamic integration of the free energy along a reaction
coordinate in cartesian coordinates.
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Y. Deng and B. Roux.
Computations of standard binding free energies with molecular
dynamics simulations.
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G. Fiorin, M. L. Klein, and J. Hénin.
Using collective variables to drive molecular dynamics simulations.
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D. Frenkel and B. Smit.
Understanding Molecular Simulation From Algorithms to
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H. Fu, X. Shao, C. Chipot, and W. Cai.
Extended adaptive biasing force algorithm. an on-the-fly
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Accelerated molecular dynamics: a promising and efficient simulation
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Multilevel summation method for electrostatic force evaluation.
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- 35
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G. D. Hawkins, C. J. Cramer, and D. G. Truhlar.
Parametrized models of aqueous free energies of solvation based on
pairwise descreening of solute atomic charges from a dielectric medium.
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Overcoming free energy barriers using unconstrained molecular
dynamics simulations.
J. Chem. Phys., 121:2904-2914, 2004.
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J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein.
Exploring multidimensional free energy landscapes using
time-dependent biases on collective variables.
J. Chem. Theory Comput., 6(1):35-47, 2010.
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Local elevation - A method for improving the searching properties
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M. Iannuzzi, A. Laio, and M. Parrinello.
Efficient exploration of reactive potential energy surfaces using
car-parrinello molecular dynamics.
Phys. Rev. Lett., 90(23):238302, 2003.
- 40
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W. Jiang, D. Hardy, J. Phillips, A. MacKerell, K. Schulten, and B. Roux.
High-performance scalable molecular dynamics simulations of a
polarizable force field based on classical Drude oscillators in NAMD.
J. Phys. Chem. Lett., 2:87-92, 2011.
- 41
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J. Kastner and W. Thiel.
Bridging the gap between thermodynamic integration and umbrella
sampling provides a novel analysis method: ``umbrella integration''.
J. Chem. Phys., 123(14):144104, 2005.
- 42
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P. M. King.
Free energy via molecular simulation: A primer.
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- 43
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J. G. Kirkwood.
Statistical mechanics of fluid mixtures.
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P. A. Kollman.
Free energy calculations: Applications to chemical and biochemical
phenomena.
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E. A. Koopman and C. P. Lowe.
Advantages of a Lowe-Andersen thermostat in molecular dynamics
simulations.
J. Chem. Phys., 124:204103, 2006.
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A. Laio and M. Parrinello.
Escaping free-energy minima.
Proc. Natl. Acad. Sci. USA, 99(20):12562-12566, 2002.
- 47
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G. Lamoureux, E. Harder, I. V. Vorobyov, B. Roux, and A. D. MacKerell.
A polarizable model of water for molecular dynamics simulations of
biomolecules.
Chem. Phys. Lett., 418(1-3):245-249, 2006.
- 48
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G. Lamoureux and B. Roux.
Modeling induced polarization with classical Drude oscillators:
Theory and molecular dynamics simulation algorithm.
J. Chem. Phys., 119(6):3025-3039, 2003.
- 49
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A. Lesage, T. Lelièvre, G. Stoltz, and J. Hénin.
Smoothed biasing forces yield unbiased free energies with the
extended-system adaptive biasing force method.
J. Phys. Chem. B.
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- 50
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N. Lu, D. A. Kofke, and T. B. Woolf.
Improving the efficiency and reliability of free energy perturbation
calculations using overlap sampling methods.
J. Comput. Chem., 25:28-39, 2004.
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Separation-shifted scaling, a new scaling method for
Lennard-Jones interactions in thermodynamic integration.
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A. E. Mark.
Free energy perturbation calculations.
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Coarse grained model for semiquantitative lipid simulations.
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Potential of mean force calculations: A multiple-walker adaptive
biasing force approach.
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Energy landscape of a small peptide revealed by dihedral angle
principal component analysis.
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Modification of the generalised born model suitable for
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Exploring protein native states and large-scale conformational
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A comparison of alternative approaches to free energy calculations.
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Efficient reconstruction of complex free energy landscapes by
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