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Index
- 1
-
M. P. Allen and D. J. Tildesley.
Computer Simulation of Liquids.
Oxford University Press, New York, 1987.
- 2
-
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.
- 3
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C. H. Bennett.
Efficient estimation of free energy differences with monte carlo
data.
J. Comp. Phys., 22:245-268, 1976.
- 4
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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.
- 5
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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.
- 6
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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.
- 7
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A. Bondi.
van der Waals volumes and radii.
J. Phys. Chem., 68:441-451, 1964.
- 8
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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.
- 9
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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.
- 10
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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.
- 11
-
G. Bussi, A. Laio, and M. Parrinello.
Equilibrium free energies from nonequilibrium metadynamics.
Phys. Rev. Lett., 96(9):090601, 2006.
- 12
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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.
- 13
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C. Chipot and D. A. Pearlman.
Free energy calculations. the long and winding gilded road.
Mol. Sim., 28:1-12, 2002.
- 14
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C. Chipot and A. Pohorille, editors.
Free energy calculations. Theory and applications in chemistry
and biology.
Springer Verlag, 2007.
- 15
-
G. Ciccotti, R. Kapral, and E. Vanden-Eijnden.
Blue moon sampling, vectorial reaction coordinates, and unbiased
constrained dynamics.
ChemPhysChem, 6(9):1809-1814, 2005.
- 16
-
E. A. Coutsias, C. Seok, and K. A. Dill.
Using quaternions to calculate RMSD.
J. Comput. Chem., 25(15):1849-1857, 2004.
- 17
-
E. Darve and A. Pohorille.
Calculating free energies using average force.
J. Chem. Phys,, 115(20):9169-9183, NOV 22 2001.
- 18
-
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.
- 19
-
W. K. den Otter.
Thermodynamic integration of the free energy along a reaction
coordinate in cartesian coordinates.
J. Chem. Phys., 112:7283-7292, 2000.
- 20
-
Y. Deng and B. Roux.
Computations of standard binding free energies with molecular
dynamics simulations.
J. Phys. Chem. B, 113(8):2234-2246, 2009.
- 21
-
D. Frenkel and B. Smit.
Understanding Molecular Simulation From Algorithms to
Applications.
Academic Press, California, 2002.
- 22
-
J. Gao, K. Kuczera, B. Tidor, and M. Karplus.
Hidden thermodynamics of mutant proteins: A molecular dynamics
analysis.
Science, 244:1069-1072, 1989.
- 23
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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.
- 24
-
H. Grubmüller.
Predicting slow structural transitions in macromolecular systems:
Conformational flooding.
Phys. Rev. E, 52(3):2893-2906, Sep 1995.
- 25
-
D. Hamelberg, C. de Oliveira, and J. McCammon.
Sampling of slow diffusive conformational transitions with
accelerated molecular dynamics.
J. Chem. Phys., 127:155102, 2007.
- 26
-
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.
- 27
-
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.
- 28
-
J. Hénin and C. Chipot.
Overcoming free energy barriers using unconstrained molecular
dynamics simulations.
J. Chem. Phys., 121:2904-2914, 2004.
- 29
-
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.
- 30
-
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.
- 31
-
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.
- 32
-
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.
- 33
-
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.
- 34
-
J. G. Kirkwood.
Statistical mechanics of fluid mixtures.
J. Chem. Phys., 3:300-313, 1935.
- 35
-
P. A. Kollman.
Free energy calculations: Applications to chemical and biochemical
phenomena.
Chem. Rev., 93:2395-2417, 1993.
- 36
-
E. A. Koopman and C. P. Lowe.
Advantages of a Lowe-Andersen thermostat in molecular dynamics
simulations.
J. Chem. Phys., 124:204103, 2006.
- 37
-
A. Laio and M. Parrinello.
Escaping free-energy minima.
Proc. Natl. Acad. Sci. USA, 99(20):12562-12566, 2002.
- 38
-
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.
- 39
-
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.
- 40
-
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.
- 41
-
S. J. Marrink, A. H. de Vries, and A. E. Mark.
Coarse grained model for semiquantitative lipid simulations.
108:750-760, 2004.
- 42
-
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.
111:7812-7824, 2007.
- 43
-
J. A. McCammon and S. C. Harvey.
Dynamics of Proteins and Nucleic Acids.
Cambridge University Press, Cambridge, 1987.
- 44
-
L. Monticelli, S. Kandasamy, X. Periole, and R. L. D. T. S. Marrink.
The martini coarse grained forcefield: extension to proteins.
4:819-834, 2008.
- 45
-
A. Onufriev, D. Bashford, and D. A. Case.
Modification of the generalised born model suitable for
macromolecules.
J. Phys. Chem., 104:3712-3720, 2000.
- 46
-
A. Onufriev, D. Bashford, and D. A. Case.
Exploring protein native states and large-scale conformational
changes with a modified generalized born model.
55:383-394, 2004.
- 47
-
D. A. Pearlman.
A comparison of alternative approaches to free energy calculations.
J. Phys. Chem., 98:1487-1493, 1994.
- 48
-
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.
- 49
-
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.
- 50
-
M. J. Ruiz-Montero, D. Frenkel, and J. J. Brey.
Efficient schemes to compute diffusive barrier crossing rates.
Mol. Phys., 90:925-941, 1997.
- 51
-
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.
- 52
-
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.
- 53
-
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.
- 54
-
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.
- 55
-
R. D. Skeel and J. J. Biesiadecki.
Symplectic integration with variable stepsize.
Ann. Numer. Math., 1:191-198, 1994.
- 56
-
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.
- 57
-
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.
- 58
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T. P. Straatsma and J. A. McCammon.
Multiconfiguration thermodynamic integration.
J. Chem. Phys., 95:1175-1118, 1991.
- 59
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T. P. Straatsma and J. A. McCammon.
Computational alchemy.
Annu. Rev. Phys. Chem., 43:407-435, 1992.
- 60
-
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.
- 61
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A. F. Voter.
Hyperdynamics: Accelerated molecular dynamics of infrequent events.
Phys. Rev. Lett., 78(20):3908-3911, May 1997.
- 62
-
Y. Wang, C. Harrison, K. Schulten, and J. McCammon.
Implementation of accelerated molecular dynamics in NAMD.
"Comp. Sci. Discov.", 4:015002, 2011.
- 63
-
R. W. Zwanzig.
High-temperature equation of state by a perturbation method. i.
nonpolar gases.
J. Chem. Phys., 22:1420-1426, 1954.
namd@ks.uiuc.edu