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M. P. Allen and D. J. Tildesley.
Computer Simulation of Liquids.
Oxford University Press, New York, 1987.

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.

C. H. Bennett.
Efficient estimation of free energy differences with monte carlo data.
J. Comp. Phys., 22:245-268, 1976.

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.

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.

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.

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.

O. Bignucolo, C. Chipot, S. Kellenberger, and B. Roux.
Galvani offset potential and constant-pH simulations of membrane proteins.
J. Phys. Chem. B, 126(36):6868-6877, 2022.
PMID: 36049129.

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

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.

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.

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.

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

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.

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

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

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

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

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.

Y. Deng and B. Roux.
Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules.
J. Phys. Chem. B, 108:16567-16576, 2004.

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

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

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.

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

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.

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.

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.

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.

W. Jiang, C. Chipot, and B. Roux.
Computing relative binding affinity of ligands to receptor: An effective hybrid single-dual-topology free-energy perturbation approach in NAMD.
J. Chem. Inf. Model., 59(9):3794-3802, 2019.

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.

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.

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.

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

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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

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.

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.

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

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.

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

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

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.

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

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.

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.

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.

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.

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

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.

S. Shobana, B. Roux, and O. S. Andersen.
Free energy simulations: Thermodynamic reversibility and variability.
J. Phys. Chem. B, 104(21):5179-5190, 2000.

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.

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.

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

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.

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

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

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.

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

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

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

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

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.

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.

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.

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

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.

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.

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.

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.

R. W. Zwanzig.
High-temperature equation of state by a perturbation method. i. nonpolar gases.
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