next up previous contents index
Next: Index Up: NAMD 2.13 User's Guide Previous: Documentation   Contents   Index

Bibliography

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
L. Biedermannová, Z. Prokop, A. Gora, E. Chovancová, M. Kovács, J. Damborsky, and R. C. Wade.
A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase linb.
Journal of Biological Chemistry, 287(34):29062-29074, 2012.

10
A. Bondi.
van der Waals volumes and radii.
J. Phys. Chem., 68:441-451, 1964.

11
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.

12
D. Branduardi, F. L. Gervasio, and M. Parrinello.
From a to b in free energy space.
J Chem Phys, 126(5):054103, 2007.

13
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.

14
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.

15
G. Bussi, D. Donadio, and M. Parrinello.
Canonical sampling through velocity rescaling.
J. Chem. Phys., 126:014101, 2007.

16
G. Bussi, A. Laio, and M. Parrinello.
Equilibrium free energies from nonequilibrium metadynamics.
Phys. Rev. Lett., 96(9):090601, 2006.

17
P. Carlsson, S. Burendahl, and L. Nilsson.
Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics.
Biophysical Journal, 91(9):3151-3161, 2006.

18
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.

19
Y. Chen and B. Roux.
Constant-pH hybrid nonequilibrium molecular dynamics-Monte Carlo simulation method.
J. Chem. Theory Comput., 11:3919-3931, 2015.

20
Y. Chen and B. Roux.
Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics-Monte Carlo simulations.
J. Chem. Phys., 142:024101, 2015.

21
C. Chipot and D. A. Pearlman.
Free energy calculations. the long and winding gilded road.
Mol. Sim., 28:1-12, 2002.

22
C. Chipot and A. Pohorille, editors.
Free energy calculations. Theory and applications in chemistry and biology.
Springer Verlag, 2007.

23
G. Ciccotti, R. Kapral, and E. Vanden-Eijnden.
Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics.
ChemPhysChem, 6(9):1809-1814, 2005.

24
V. Cojocaru, P. J. Winn, and R. C. Wade.
Multiple, ligand-dependent routes from the active site of cytochrome P450 2C9.
Current Drug Metabolism, 13(2):143-154, 2012.

25
J. Comer, J. Phillips, K. Schulten, and C. Chipot.
Multiple-walker strategies for free-energy calculations in namd: Shared adaptive biasing force and walker selection rules.
J. Chem. Theor. Comput., 10:5276-5285, 2014.

26
E. A. Coutsias, C. Seok, and K. A. Dill.
Using quaternions to calculate RMSD.
J. Comput. Chem., 25(15):1849-1857, 2004.

27
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.

28
W. K. den Otter.
Thermodynamic integration of the free energy along a reaction coordinate in cartesian coordinates.
J. Chem. Phys., 112:7283-7292, 2000.

29
Y. Deng and B. Roux.
Computations of standard binding free energies with molecular dynamics simulations.
J. Phys. Chem. B, 113(8):2234-2246, 2009.

30
G. Fiorin, M. L. Klein, and J. Hénin.
Using collective variables to drive molecular dynamics simulations.
Mol. Phys., 111(22-23):3345-3362, 2013.

31
D. Frenkel and B. Smit.
Understanding Molecular Simulation From Algorithms to Applications.
Academic Press, California, 2002.

32
H. Fu, X. Shao, C. Chipot, and W. Cai.
Extended adaptive biasing force algorithm. an on-the-fly implementation for accurate free-energy calculations.
J. Chem. Theory Comput., 2016.

33
J. Gao, K. Kuczera, B. Tidor, and M. Karplus.
Hidden thermodynamics of mutant proteins: A molecular dynamics analysis.
Science, 244:1069-1072, 1989.

34
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.

35
N. M. Glykos.
Carma: a molecular dynamics analysis program.
J. Comput. Chem., 27(14):1765-1768, 2006.

36
H. Grubmüller.
Predicting slow structural transitions in macromolecular systems: Conformational flooding.
Phys. Rev. E, 52(3):2893-2906, Sep 1995.

37
D. Hamelberg, C. de Oliveira, and J. McCammon.
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics.
J. Chem. Phys., 127:155102, 2007.

38
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.

39
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. Theory Comput., 2(6):1587-1597, 2006.

40
D. J. Hardy, Z. Wu, J. C. Phillips, J. E. Stone, R. D. Skeel, and K. Schulten.
Multilevel summation method for electrostatic force evaluation.
J. Chem. Theory Comput., 11:766-779, 2015.

41
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.

42
J. Hénin and C. Chipot.
Overcoming free energy barriers using unconstrained molecular dynamics simulations.
J. Chem. Phys., 121:2904-2914, 2004.

43
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.

44
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.

45
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.

46
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.

47
S. Jo and W. Jiang.
A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations.
197:304-311, 2015.

48
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.

49
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.

50
J. G. Kirkwood.
Statistical mechanics of fluid mixtures.
J. Chem. Phys., 3:300-313, 1935.

51
D. B. Kokh, M. Amaral, J. Bomke, U. Grädler, D. Musil, H.-P. Buchstaller, M. K. Dreyer, M. Frech, M. Lowinski, F. Vallee, M. Bianciotto, A. Rak, and R. C. Wade.
Estimation of drug-target residence times by $ \tau$ -random acceleration molecular dynamics simulations.
Journal of Chemical Theory and Computation, 14(7):3859-3869, 2018.
PMID: 29768913.

52
P. A. Kollman.
Free energy calculations: Applications to chemical and biochemical phenomena.
Chem. Rev., 93:2395-2417, 1993.

53
E. A. Koopman and C. P. Lowe.
Advantages of a Lowe-Andersen thermostat in molecular dynamics simulations.
J. Chem. Phys., 124:204103, 2006.

54
A. Laio and M. Parrinello.
Escaping free-energy minima.
Proc. Natl. Acad. Sci. USA, 99(20):12562-12566, 2002.

55
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.

56
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.

57
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, 121(15):3676-3685, 2017.

58
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.

59
S. K. Lüdemann, V. Lounnas, and R. C. Wade.
How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. random expulsion molecular dynamics investigation of ligand access channels and mechanisms.
Journal of Molecular Biology, 303(5):797-811, 2000.

60
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.

61
J. D. C. Maia, G. A. Urquiza Carvalho, C. P. Mangueira Jr, S. R. Santana, L. A. F. Cabral, and G. B. Rocha.
Gpu linear algebra libraries and gpgpu programming for accelerating mopac semiempirical quantum chemistry calculations.
J. Chem. Theory Comput., 8(9):3072-3081, 2012.

62
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.

63
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.

64
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.

65
J. A. McCammon and S. C. Harvey.
Dynamics of Proteins and Nucleic Acids.
Cambridge University Press, Cambridge, 1987.

66
M. Melo, R. Bernardi, T. Rudack, M. Scheurer, C. Riplinger, J. Phillips, J. Maia, G. Rocha, J. Ribeiro, J. Stone, F. Nesse, K. Schulten, and Z. Luthey-Schulten.
NAMD goes quantum: An integrative suite for QM/MM simulations.
Nat. Methods, 15:351-354, 2018.

67
Y. Miao, V. Feher, and J. McCammon.
Gaussian accelerated molecular dynamics: Unconstrained enhanced sampling and free energy calculation.
J. Chem. Theory Comput., 11:3584-3595, 2015.

68
K. Minoukadeh, C. Chipot, and T. Lelièvre.
Potential of mean force calculations: A multiple-walker adaptive biasing force approach.
J. Chem. Theor. Comput., 6:1008-1017, 2010.

69
L. Monticelli, S. Kandasamy, X. Periole, and R. L. D. T. S. Marrink.
The martini coarse grained forcefield: extension to proteins.
J. Chem. Theory Comput., 4:819-834, 2008.

70
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.

71
F. Neese.
The ORCA program system.
Wiley Interdiscip. Rev.: Comput. Mol. Sci., 2:73-78, 2012.

72
J. P. Nilmeier, G. E. Crooks, D. D. L. Minh, and J. D. Chodera.
Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.
Proc. Natl. Acad. Sci. USA, 108:E1009-E1018, 2011.

73
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.

74
A. Onufriev, D. Bashford, and D. A. Case.
Modification of the generalised born model suitable for macromolecules.
J. Phys. Chem., 104:3712-3720, 2000.

75
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.

76
Y. Pang, Y. Miao, Y. Wang, and J. McCammon.
Gaussian accelerated molecular dynamics in NAMD.
J. Chem. Theory Comput., 13:9-19, 2017.

77
D. A. Pearlman.
A comparison of alternative approaches to free energy calculations.
J. Phys. Chem., 98:1487-1493, 1994.

78
J. W. Pitera and J. D. Chodera.
On the use of experimental observations to bias simulated ensembles.
J. Chem. Theory Comput., 8:3445-3451, 2012.

79
B. K. Radak, C. Chipot, D. Suh, S. Jo, W. Jiang, J. C. Phillips, K. Schulten, and B. Roux.
Constant-pH molecular dynamics simulations for large biomolecular systems.
J. Chem. Theory Comput., 13:5933-5944, 2017.

80
B. K. Radak and B. Roux.
Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations.
J. Chem. Phys., 145:134109, 2016.

81
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.

82
J. V. Ribeiro, R. C. Bernardi, T. Rudack, J. E. Stone, J. C. Phillips, P. L. Freddolino, and K. Schulten.
QwikMD-integrative molecular dynamics toolkit for novices and experts.
Sci. Rep., 6:26536, 2016.

83
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.

84
M. J. Ruiz-Montero, D. Frenkel, and J. J. Brey.
Efficient schemes to compute diffusive barrier crossing rates.
Mol. Phys., 90:925-941, 1997.

85
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.

86
K. Schleinkofer, P. J. Winn, S. K. Lüdemann, R. C. Wade, et al.
Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?
EMBO Reports, 6(6):584-589, 2005.

87
H. M. Senn and W. Thiel.
Qm/mm methods for biomolecular systems.
Angew. Chem. Int. Ed. Engl., 48(7):1198-1229, 2009.

88
R. Shen, W. Han, G. Fiorin, S. M. Islam, K. Schulten, and B. Roux.
Structural refinement of proteins by restrained molecular dynamics simulations with non-interacting molecular fragments.
PLoS Comput. Biol., 11(10):e1004368, 2015.

89
M. R. Shirts, D. L. Mobley, J. D. Chodera, and V. S. Pande.
Accurate and efficient corrections for missing dispersion interactions in molecular simulations.
J. Phys. Chem. B, 111(45):13052-13063, 2007.

90
C. Simmerling, T. Fox, and P. A. Kollman.
Use of locally enhanced sampling in free energy calculations: Testing and application to the $ \alpha\rightarrow\beta$ anomerization of glucose.
J. Am. Chem. Soc., 120(23):5771-5782, 1998.

91
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.

92
R. D. Skeel and J. J. Biesiadecki.
Symplectic integration with variable stepsize.
Ann. Numer. Math., 1:191-198, 1994.

93
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 eff˘Ć░čects.
Theor Chem Acc, 101:426-434, 1999.

94
H. A. Stern.
Molecular simulation with variable protonation states at constant pH.
J. Chem. Phys., 126:164112, 2007.

95
J. J. Stewart.
Mopac: a semiempirical molecular orbital program.
J. Comp.-Aided Mol. Design, 4(1):1-103, 1990.

96
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.

97
T. P. Straatsma and J. A. McCammon.
Multiconfiguration thermodynamic integration.
J. Chem. Phys., 95:1175-1118, 1991.

98
T. P. Straatsma and J. A. McCammon.
Computational alchemy.
Annu. Rev. Phys. Chem., 43:407-435, 1992.

99
B. T. Thole.
Molecular polarizabilities calculated with a modified dipole interaction.
Chem. Phys., 59:341-350, 1981.

100
P. Van Duijnen and M. Swart.
Molecular and atomic polarizabilities: Thole's model revisited.
J. Phys. Chem. A, 102(14):2399-2407, 1998.

101
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.

102
H. Vashisth and C. F. Abrams.
Ligand escape pathways and (un) binding free energy calculations for the hexameric insulin-phenol complex.
Biophysical Journal, 95(9):4193-4204, 2008.

103
L. Wang, R. A. Friesner, and B. J. Berne.
Replica exchange with solute scaling: A more efficient version of replica exchange with solute tempering (REST2).
J. Phys. Chem. B, 115(30):9431-9438, 2011.

104
Y. Wang, C. Harrison, K. Schulten, and J. McCammon.
Implementation of accelerated molecular dynamics in NAMD.
"Comp. Sci. Discov.", 4:015002, 2011.

105
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.

106
A. D. White and G. A. Voth.
Efficient and minimal method to bias molecular simulations with experimental data.
J. Chem. Theory Comput., ASAP, 2014.

107
P. C. Whitford, J. K. Noel, S. Gosavi, A. Schug, K. Y. Sanbonmatsu, and J. N. Onuchic.
An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields.
Proteins, 75(2):430-441, 2009.

108
P. C. Whitford, A. Schug, J. Saunders, S. P. Hennelly, J. N. Onuchic, and K. Y. Sanbonmatsu.
Nonlocal helix formation is key to understanding s-adenosylmethionine-1 riboswitch function.
Biophysical Journal, 96(2):L7 - L9, 2009.

109
P. J. Winn, S. K. Lüdemann, R. Gauges, V. Lounnas, and R. C. Wade.
Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine.
Proceedings of the National Academy of Sciences, 99(8):5361-5366, 2002.

110
L. Zheng and W. Yang.
Practically efficient and robust free energy calculations: Double-integration orthogonal space tempering.
J. Chem. Theor. Compt., 8:810-823, 2012.

111
R. W. Zwanzig.
High-temperature equation of state by a perturbation method. i. nonpolar gases.
J. Chem. Phys., 22:1420-1426, 1954.



http://www.ks.uiuc.edu/Research/namd/