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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.
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.
Phys. Rev. Lett., 100:020603, 2008.
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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
macromolecular structures.
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D. L. Beveridge and F. M. DiCapua.
Free energy via molecular simulation: Applications to chemical and
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A. Bondi.
van der Waals volumes and radii.
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S. Boresch and M. Karplus.
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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B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan,
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CHARMM: a program for macromolecular energy, minimization, and
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G. Bussi, A. Laio, and M. Parrinello.
Equilibrium free energies from nonequilibrium metadynamics.
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Constrained reaction coordinate dynamics for the simulation of rare
events.
Chem. Phys. Lett., 156:472-477, 1989.
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C. Chipot and D. A. Pearlman.
Free energy calculations. the long and winding gilded road.
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C. Chipot and A. Pohorille, editors.
Free energy calculations. Theory and applications in chemistry
and biology.
Springer Verlag, 2007.
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G. Ciccotti, R. Kapral, and E. Vanden-Eijnden.
Blue moon sampling, vectorial reaction coordinates, and unbiased
constrained dynamics.
ChemPhysChem, 6(9):1809-1814, 2005.
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E. A. Coutsias, C. Seok, and K. A. Dill.
Using quaternions to calculate RMSD.
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E. Darve, D. Rodríguez-Gómez, and A. Pohorille.
Adaptive biasing force method for scalar and vector free energy
calculations.
J. Chem. Phys., 128(14):144120, 2008.
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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.
Mol. Phys., 111(22-23):3345-3362, 2013.
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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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Predicting slow structural transitions in macromolecular systems:
Conformational flooding.
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D. Hamelberg, C. de Oliveira, and J. McCammon.
Sampling of slow diffusive conformational transitions with
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Accelerated molecular dynamics: a promising and efficient simulation
method for biomolecules.
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Multilevel summation method for electrostatic force evaluation.
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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.
- 36
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T. Huber, A. E. Torda, and W. van Gunsteren.
Local elevation - A method for improving the searching properties
of molecular-dynamics simulation.
Journal of Computer-Aided Molecular Design, 8(6):695-708, DEC
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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.
- 38
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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.
- 39
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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
experimental applications, volume 2, pages 267-314. ESCOM, Leiden, 1993.
- 40
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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.
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A. Laio and M. Parrinello.
Escaping free-energy minima.
Proc. Natl. Acad. Sci. USA, 99(20):12562-12566, 2002.
- 44
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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.
- 45
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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.
- 46
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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.
- 47
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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.
In P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A.
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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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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.
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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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GROMACS.
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Modification of the generalised born model suitable for
macromolecules.
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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
multiple walkers metadynamics.
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Modeling side chains in peptides and proteins: Application of the
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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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Efficient and minimal method to bias molecular simulations with
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