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Index
- 1
-
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.
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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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F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, J. E. F. Meyer, M. D. Brice,
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The protein data bank: A computer-based archival file for
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Constrained reaction coordinate dynamics for the simulation of rare
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Free energy calculations. Theory and applications in chemistry
and biology.
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G. Ciccotti, R. Kapral, and E. Vanden-Eijnden.
Blue moon sampling, vectorial reaction coordinates, and unbiased
constrained dynamics.
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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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D. Frenkel and B. Smit.
Understanding Molecular Simulation From Algorithms to
Applications.
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Carma: a molecular dynamics analysis program.
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Conformational flooding.
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Sampling of slow diffusive conformational transitions with
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Accelerated molecular dynamics: a promising and efficient simulation
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for a polarizable force field based on the classical drude oscillator.
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pairwise descreening of solute atomic charges from a dielectric medium.
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Overcoming free energy barriers using unconstrained molecular
dynamics simulations.
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Exploring multidimensional free energy landscapes using
time-dependent biases on collective variables.
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Local elevation - A method for improving the searching properties
of molecular-dynamics simulation.
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Efficient exploration of reactive potential energy surfaces using
car-parrinello molecular dynamics.
Phys. Rev. Lett., 90(23):238302, 2003.
- 35
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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.
- 36
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P. M. King.
Free energy via molecular simulation: A primer.
In W. F. Van Gunsteren, P. K. Weiner, and A. J. Wilkinson, editors,
Computer simulation of biomolecular systems: Theoretical and
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- 37
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J. G. Kirkwood.
Statistical mechanics of fluid mixtures.
J. Chem. Phys., 3:300-313, 1935.
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P. A. Kollman.
Free energy calculations: Applications to chemical and biochemical
phenomena.
Chem. Rev., 93:2395-2417, 1993.
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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.
- 40
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A. Laio and M. Parrinello.
Escaping free-energy minima.
Proc. Natl. Acad. Sci. USA, 99(20):12562-12566, 2002.
- 41
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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.
- 42
-
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.
- 43
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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.
- 44
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Separation-shifted scaling, a new scaling method for
Lennard-Jones interactions in thermodynamic integration.
J. Chem. Phys., 100:9025-9031, 1994.
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A. E. Mark.
Free energy perturbation calculations.
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- 46
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S. J. Marrink, A. H. de Vries, and A. E. Mark.
Coarse grained model for semiquantitative lipid simulations.
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- 47
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S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. de Vries.
The martini forcefield: coarse grained model for biomolecular
simulations.
J. Phys. Chem. B, 111:7812-7824, 2007.
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J. A. McCammon and S. C. Harvey.
Dynamics of Proteins and Nucleic Acids.
Cambridge University Press, Cambridge, 1987.
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L. Monticelli, S. Kandasamy, X. Periole, and R. L. D. T. S. Marrink.
The martini coarse grained forcefield: extension to proteins.
J. Chem. Theor. Comp., 4:819-834, 2008.
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Y. Mu, P. H. Nguyen, and G. Stock.
Energy landscape of a small peptide revealed by dihedral angle
principal component analysis.
Proteins, 58(1):45-52, 2005.
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J. K. Noel, P. C. Whitford, K. Y. Sanbonmatsu, and J. N. Onuchic.
SMOG@ctbp: simplified deployment of structure-based models in
GROMACS.
Nucleic Acids Research, 38:W657-61, 2010.
- 52
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A. Onufriev, D. Bashford, and D. A. Case.
Modification of the generalised born model suitable for
macromolecules.
J. Phys. Chem., 104:3712-3720, 2000.
- 53
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A. Onufriev, D. Bashford, and D. A. Case.
Exploring protein native states and large-scale conformational
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Symplectic integration with variable stepsize.
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Implementation of accelerated molecular dynamics in NAMD.
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Approximate atomic surfaces from linear combinations of pairwise
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http://www.ks.uiuc.edu/Research/namd/