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     Index 
- 1
 - 
M. P. Allen and D. J. Tildesley.
Computer Simulation of Liquids.
Oxford University Press, New York, 1987.
 - 2
 - 
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.
 - 3
 - 
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.
 - 4
 - 
A. Barducci, G. Bussi, and M. Parrinello.
Well-tempered metadynamics: A smoothly converging and tunable
  free-energy method.
Phys. Rev. Lett., 100:020603, 2008.
 - 5
 - 
C. H. Bennett.
Efficient estimation of free energy differences with monte carlo
  data.
J. Comp. Phys., 22:245-268, 1976.
 - 6
 - 
F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, J. E. F. Meyer, M. D. Brice,
  J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi.
The protein data bank: A computer-based archival file for
  macromolecular structures.
J. Mol. Biol., 112:535-542, 1977.
 - 7
 - 
T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, and W. F. van
  Gunsteren.
Avoiding singularities and numerical instabilities in free energy
  calculations based on molecular simulations.
Chem. Phys. Lett., 222:529-539, 1994.
 - 8
 - 
D. L. Beveridge and F. M. DiCapua.
Free energy via molecular simulation: Applications to chemical and
  biomolecular systems.
Annu. Rev. Biophys. Biophys., 18:431-492, 1989.
 - 9
 - 
A. Bondi.
van der Waals volumes and radii.
J. Phys. Chem., 68:441-451, 1964.
 - 10
 - 
S. Boresch and M. Karplus.
The role of bonded terms in free energy simulations: I. theoretical
  analysis.
J. Phys. Chem. A, 103:103-118, 1999.
 - 11
 - 
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan,
  and M. Karplus.
CHARMM: a program for macromolecular energy, minimization, and
  dynamics calculations.
J. Comp. Chem., 4(2):187-217, 1983.
 - 12
 - 
A. T. Brünger.
X-PLOR, Version 3.1, A System for X-ray Crystallography and
  NMR.
The Howard Hughes Medical Institute and Department of Molecular
  Biophysics and Biochemistry, Yale University, 1992.
 - 13
 - 
G. Bussi, A. Laio, and M. Parrinello.
Equilibrium free energies from nonequilibrium metadynamics.
Phys. Rev. Lett., 96(9):090601, 2006.
 - 14
 - 
A. Carter, E, G. Ciccotti, J. T. Hynes, and R. Kapral.
Constrained reaction coordinate dynamics for the simulation of rare
  events.
Chem. Phys. Lett., 156:472-477, 1989.
 - 15
 - 
C. Chipot and D. A. Pearlman.
Free energy calculations. the long and winding gilded road.
Mol. Sim., 28:1-12, 2002.
 - 16
 - 
C. Chipot and A. Pohorille, editors.
Free energy calculations. Theory and applications in chemistry
  and biology.
Springer Verlag, 2007.
 - 17
 - 
G. Ciccotti, R. Kapral, and E. Vanden-Eijnden.
Blue moon sampling, vectorial reaction coordinates, and unbiased
  constrained dynamics.
ChemPhysChem, 6(9):1809-1814, 2005.
 - 18
 - 
E. A. Coutsias, C. Seok, and K. A. Dill.
Using quaternions to calculate RMSD.
J. Comput. Chem., 25(15):1849-1857, 2004.
 - 19
 - 
E. Darve and A. Pohorille.
Calculating free energies using average force.
J. Chem. Phys,, 115(20):9169-9183, NOV 22 2001.
 - 20
 - 
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.
 - 21
 - 
W. K. den Otter.
Thermodynamic integration of the free energy along a reaction
  coordinate in cartesian coordinates.
J. Chem. Phys., 112:7283-7292, 2000.
 - 22
 - 
Y. Deng and B. Roux.
Computations of standard binding free energies with molecular
  dynamics simulations.
J. Phys. Chem. B, 113(8):2234-2246, 2009.
 - 23
 - 
D. Frenkel and B. Smit.
Understanding Molecular Simulation From Algorithms to
  Applications.
Academic Press, California, 2002.
 - 24
 - 
J. Gao, K. Kuczera, B. Tidor, and M. Karplus.
Hidden thermodynamics of mutant proteins: A molecular dynamics
  analysis.
Science, 244:1069-1072, 1989.
 - 25
 - 
M. K. Gilson, J. A. Given, B. L. Bush, and J. A. McCammon.
The statistical-thermodynamic basis for computation of binding
  affinities: A critical review.
Biophys. J., 72:1047-1069, 1997.
 - 26
 - 
N. M. Glykos.
Carma: a molecular dynamics analysis program.
J. Comput. Chem., 27(14):1765-1768, 2006.
 - 27
 - 
H. Grubmüller.
Predicting slow structural transitions in macromolecular systems:
  Conformational flooding.
Phys. Rev. E, 52(3):2893-2906, Sep 1995.
 - 28
 - 
D. Hamelberg, C. de Oliveira, and J. McCammon.
Sampling of slow diffusive conformational transitions with
  accelerated molecular dynamics.
J. Chem. Phys., 127:155102, 2007.
 - 29
 - 
D. Hamelberg, J. Mongan, and J. McCammon.
Accelerated molecular dynamics: a promising and efficient simulation
  method for biomolecules.
J. Chem. Phys., 120(24):11919-11929, 2004.
 - 30
 - 
E. Harder, V. M. Anisimov, I. V. Vorobyov, P. E. M. Lopes, S. Y. Noskov, A. D.
  MacKerell, and B. Roux.
Atomic level anisotropy in the electrostatic modeling of lone pairs
  for a polarizable force field based on the classical drude oscillator.
J. Chem. Theor. Comp., 2(6):1587-1597, 2006.
 - 31
 - 
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.
J. Phys. Chem., 100:19824-19839, 1996.
 - 32
 - 
J. Hénin and C. Chipot.
Overcoming free energy barriers using unconstrained molecular
  dynamics simulations.
J. Chem. Phys., 121:2904-2914, 2004.
 - 33
 - 
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.
 - 34
 - 
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
  1994.
 - 35
 - 
G. Hummer and I. Kevrekidis.
Coarse molecular dynamics of a peptide fragment: Free energy,
  kinetics, and long-time dynamics computations.
Journal of Chemical Physics, 118(23):10762 - 10773, JUN 15
  2003.
 - 36
 - 
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.
 - 37
 - 
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.
 - 38
 - 
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.
 - 39
 - 
J. G. Kirkwood.
Statistical mechanics of fluid mixtures.
J. Chem. Phys., 3:300-313, 1935.
 - 40
 - 
P. A. Kollman.
Free energy calculations: Applications to chemical and biochemical
  phenomena.
Chem. Rev., 93:2395-2417, 1993.
 - 41
 - 
E. A. Koopman and C. P. Lowe.
Advantages of a Lowe-Andersen thermostat in molecular dynamics
  simulations.
J. Chem. Phys., 124:204103, 2006.
 - 42
 - 
A. Laio and M. Parrinello.
Escaping free-energy minima.
Proc. Natl. Acad. Sci. USA, 99(20):12562-12566, 2002.
 - 43
 - 
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.
 - 44
 - 
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.
 - 45
 - 
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.
 - 46
 - 
Z. M., T. P. Straatsma, and M. J. A.
Separation-shifted scaling, a new scaling method for
  Lennard-Jones interactions in thermodynamic integration.
J. Chem. Phys., 100:9025-9031, 1994.
 - 47
 - 
A. E. Mark.
Free energy perturbation calculations.
In P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A.
  Kollman, H. F. Schaefer III, and P. R. Schreiner, editors, Encyclopedia
  of computational chemistry, volume 2, pages 1070-1083. Wiley and Sons,
  Chichester, 1998.
 - 48
 - 
S. J. Marrink, A. H. de Vries, and A. E. Mark.
Coarse grained model for semiquantitative lipid simulations.
J. Phys. Chem. B, 108:750-760, 2004.
 - 49
 - 
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.
 - 50
 - 
J. A. McCammon and S. C. Harvey.
Dynamics of Proteins and Nucleic Acids.
Cambridge University Press, Cambridge, 1987.
 - 51
 - 
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.
 - 52
 - 
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.
 - 53
 - 
A. Onufriev, D. Bashford, and D. A. Case.
Modification of the generalised born model suitable for
  macromolecules.
J. Phys. Chem., 104:3712-3720, 2000.
 - 54
 - 
A. Onufriev, D. Bashford, and D. A. Case.
Exploring protein native states and large-scale conformational
  changes with a modified generalized born model.
Proteins: Struct., Func., Gen., 55:383-394, 2004.
 - 55
 - 
D. A. Pearlman.
A comparison of alternative approaches to free energy calculations.
J. Phys. Chem., 98:1487-1493, 1994.
 - 56
 - 
P. Raiteri, A. Laio, F. L. Gervasio, C. Micheletti, and M. Parrinello.
Efficient reconstruction of complex free energy landscapes by
  multiple walkers metadynamics.
J. Phys. Chem. B, 110(8):3533-9, 2005.
 - 57
 - 
A. Roitberg and R. Elber.
Modeling side chains in peptides and proteins: Application of the
  locally enhanced sampling technique and the simulated annealing methods to
  find minimum energy conformations.
J. Chem. Phys., 95:9277-9287, 1991.
 - 58
 - 
M. J. Ruiz-Montero, D. Frenkel, and J. J. Brey.
Efficient schemes to compute diffusive barrier crossing rates.
Mol. Phys., 90:925-941, 1997.
 - 59
 - 
M. Schaefer and C. Froemmel.
A precise analytical method for calculating the electrostatic energy
  of macromolecules in aqueous solution.
J. Mol. Biol., 216:1045-1066, 1990.
 - 60
 - 
M. R. Shirts, D. L. Mobley, J. D. Chodera, and V. S. Pande.
Accurate and efficient corrections for missing dispersion
  interactions in molecular simulations.
The Journal of Physical Chemistry B, 111(45):13052-13063,
  2007.
 - 61
 - 
C. Simmerling, T. Fox, and P. A. Kollman.
Use of locally enhanced sampling in free energy calculations:
  Testing and application to the 
 anomerization of
  glucose.
J. Am. Chem. Soc., 120(23):5771-5782, 1998.
 - 62
 - 
C. Simmerling, M. R. Lee, A. R. Ortiz, A. Kolinski, J. Skolnick, and P. A.
  Kollman.
Combining MONSSTER and LES/PME to predict protein structure from
  amino acid sequence: Application to the small protein CMTI-1.
J. Am. Chem. Soc., 122(35):8392-8402, 2000.
 - 63
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R. D. Skeel and J. J. Biesiadecki.
Symplectic integration with variable stepsize.
Ann. Numer. Math., 1:191-198, 1994.
 - 64
 - 
J. Srinivasan, M. W. Trevathan, P. Beroza, and D. A. Case.
Application of a pairwise generalized born model to proteins and
  nucleic acids: inclusion of salt effects.
Theor Chem Acc, 101:426-434, 1999.
 - 65
 - 
W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson.
Semianalytical treatment of solvation for molecular mechanics and
  dynamics.
J. Am. Chem. Soc., 112:6127-6129, 1990.
 - 66
 - 
T. P. Straatsma and J. A. McCammon.
Multiconfiguration thermodynamic integration.
J. Chem. Phys., 95:1175-1118, 1991.
 - 67
 - 
T. P. Straatsma and J. A. McCammon.
Computational alchemy.
Annu. Rev. Phys. Chem., 43:407-435, 1992.
 - 68
 - 
B. T. Thole.
Molecular polarizabilities calculated with a modified dipole
  interaction.
Chem. Phys., 59:341-350, 1981.
 - 69
 - 
P. Van Duijnen and M. Swart.
Molecular and atomic polarizabilities: Thole's model revisited.
J. Phys. Chem. A, 102(14):2399-2407, 1998.
 - 70
 - 
W. F. van Gunsteren.
Methods for calculation of free energies and binding constants:
  Successes and problems.
In W. F. Van Gunsteren and P. K. Weiner, editors, Computer
  simulation of biomolecular systems: Theoretical and experimental
  applications, pages 27-59. Escom, The Netherlands, 1989.
 - 71
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A. F. Voter.
Hyperdynamics: Accelerated molecular dynamics of infrequent events.
Phys. Rev. Lett., 78(20):3908-3911, May 1997.
 - 72
 - 
Y. Wang, C. Harrison, K. Schulten, and J. McCammon.
Implementation of accelerated molecular dynamics in NAMD.
"Comp. Sci. Discov.", 4:015002, 2011.
 - 73
 - 
J. Weiser, P. Senkin, and W. C. Still.
Approximate atomic surfaces from linear combinations of pairwise
  overlaps (LCPO).
J. Comp. Chem., 20:217-230, 1999.
 - 74
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R. W. Zwanzig.
High-temperature equation of state by a perturbation method. i.
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J. Chem. Phys., 22:1420-1426, 1954.
 
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