Bibliography

¹ H. Bekker, H.J.C. Berendsen, E.J. Dijkstra, S. Achterop, R. van Drunen, D. van der Spoel, A. Sijbers, and H. Keegstra et al., “Gromacs: A parallel computer for molecular dynamics simulations”; pp. 252–256 in Physics computing 92. Edited by R.A. de Groot and J. Nadrchal. World Scientific, Singapore, 1993.

² H.J.C. Berendsen, D. van der Spoel, and R. van Drunen, “GROMACS: A message-passing parallel molecular dynamics implementation,” Comp. Phys. Comm., 91 43–56 (1995).

³ E. Lindahl, B. Hess, and D. van der Spoel, “GROMACS 3.0: A package for molecular simulation and trajectory analysis,” J. Mol. Mod., 7 306–317 (2001).

⁴ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J.C. Berendsen, “GROMACS: Fast, Flexible and Free,” J. Comp. Chem., 26 1701–1718 (2005).

⁵ B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, “GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation,” J. Chem. Theory Comput., 4 [3] 435–447 (2008).

⁶ S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M.R. Shirts, and J.C. Smith et al., “GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit,” Bioinformatics, 29 [7] 845–854 (2013).

⁷ S. Páll, M.J. Abraham, C. Kutzner, B. Hess, and E. Lindahl, “Tackling exascale software challenges in molecular dynamics simulations with GROMACS”; pp. 3–27 in Solving software challenges for exascale. Edited by S. Markidis and E. Laure. Springer International Publishing Switzerland, London, 2015.

⁸ M.J. Abraham, T. Murtola, R. Schulz, S. Páll, J.C. Smith, B. Hess, and E. Lindahl, “GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers,” SoftwareX, 1–2 19–25 (2015).

⁹ W.F. van Gunsteren and H.J.C. Berendsen, “Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry,” Angew. Chem. Int. Ed. Engl., 29 992–1023 (1990).

¹⁰ J.G.E.M. Fraaije, “Dynamic density functional theory for microphase separation kinetics of block copolymer melts,” J. Chem. Phys., 99 9202–9212 (1993).

¹¹ D.A. McQuarrie, Statistical mechanics. Harper & Row, New York, 1976.

¹² W.F. van Gunsteren and H.J.C. Berendsen, “Algorithms for macromolecular dynamics and constraint dynamics,” Mol. Phys., 34 1311–1327 (1977).

¹³ W.F. van Gunsteren and M. Karplus, “Effect of constraints on the dynamics of macromolecules,” Macromolecules, 15 1528–1544 (1982).

¹⁴ T. Darden, D. York, and L. Pedersen, “Particle mesh Ewald: An N\(\bullet\)log(N) method for Ewald sums in large systems,” J. Chem. Phys., 98 10089–10092 (1993).

¹⁵ U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen, “A smooth particle mesh ewald potential,” J. Chem. Phys., 103 8577–8592 (1995).

¹⁶ S. Geman and D. Geman, “Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images,” IEEE Trans. Patt. Anal. Mach. Int., 6 721 (1984).

¹⁷ M. Nilges, G.M. Clore, and A.M. Gronenborn, “Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms,” FEBS Lett., 239 129–136 (1988).

¹⁸ R.C. van Schaik, H.J.C. Berendsen, A.E. Torda, and W.F. van Gunsteren, “A structure refinement method based on molecular dynamics in 4 spatial dimensions,” J. Mol. Biol., 234 751–762 (1993).

¹⁹ K. Zimmerman, “All purpose molecular mechanics simulator and energy minimizer,” J. Comp. Chem., 12 310–319 (1991).

²⁰ D.J. Adams, E.M. Adams, and G.J. Hills, “The computer simulation of polar liquids,” Mol. Phys., 38 387–400 (1979).

²¹ H. Bekker, E.J. Dijkstra, M.K.R. Renardus, and H.J.C. Berendsen, “An efficient, box shape independent non-bonded force and virial algorithm for molecular dynamics,” Mol. Sim., 14 137–152 (1995).

²² R.W. Hockney, S.P. Goel, and J. Eastwood, “Quiet High Resolution Computer Models of a Plasma,” J. Comp. Phys., 14 148–158 (1974).

²³ L. Verlet., “Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules,” Phys. Rev., 159 98–103 (1967).

²⁴ H.J.C. Berendsen and W.F. van Gunsteren, “Practical algorithms for dynamics simulations”; in 1986.

²⁵ W.C. Swope, H.C. Andersen, P.H. Berens, and K.R. Wilson, “A computer-simulation method for the calculation of equilibrium-constants for the formation of physical clusters of molecules: Application to small water clusters,” J. Chem. Phys., 76 637–649 (1982).

²⁶ H.J.C. Berendsen, J.P.M. Postma, A. DiNola, and J.R. Haak, “Molecular dynamics with coupling to an external bath,” J. Chem. Phys., 81 3684–3690 (1984).

²⁷ H.C. Andersen, “Molecular dynamics simulations at constant pressure and/or temperature,” J. Chem. Phys., 72 2384 (1980).

²⁸ S. Nosé, “A molecular dynamics method for simulations in the canonical ensemble,” Mol. Phys., 52 255–268 (1984).

²⁹ W.G. Hoover, “Canonical dynamics: Equilibrium phase-space distributions,” Phys. Rev. **A**, 31 1695–1697 (1985).

³⁰ G. Bussi, D. Donadio, and M. Parrinello, “Canonical sampling through velocity rescaling,” J. Chem. Phys., 126 014101 (2007).

³¹ H.J.C. Berendsen, “Transport properties computed by linear response through weak coupling to a bath”; pp. 139–155 in Computer simulations in material science. Edited by M. Meyer and V. Pontikis. Kluwer, 1991.

³² J.E. Basconi and M.R. Shirts, “Effects of temperature control algorithms on transport properties and kinetics in molecular dynamics simulations,” J. Chem. Theory Comput., 9 [7] 2887–2899 (2013).

³³ B. Cooke and S.J. Schmidler, “Preserving the Boltzmann ensemble in replica-exchange molecular dynamics,” J. Chem. Phys., 129 164112 (2008).

³⁴ G.J. Martyna, M.L. Klein, and M.E. Tuckerman, “Nosé-Hoover chains: The canonical ensemble via continuous dynamics,” J. Chem. Phys., 97 2635–2643 (1992).

³⁵ G.J. Martyna, M.E. Tuckerman, D.J. Tobias, and M.L. Klein, “Explicit reversible integrators for extended systems dynamics,” Mol. Phys., 87 1117–1157 (1996).

³⁶ B.L. Holian, A.F. Voter, and R. Ravelo, “Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nosé-Hoover dynamics,” Phys. Rev. E, 52 [3] 2338–2347 (1995).

³⁷ M.P. Eastwood, K.A. Stafford, R.A. Lippert, M.Ø. Jensen, P. Maragakis, C. Predescu, R.O. Dror, and D.E. Shaw, “Equipartition and the calculation of temperature in biomolecular simulations,” J. Chem. Theory Comput., ASAP DOI: 10.1021/ct9002916 (2010).

³⁸ M. Parrinello and A. Rahman, “Polymorphic transitions in single crystals: A new molecular dynamics method,” J. Appl. Phys., 52 7182–7190 (1981).

³⁹ S. Nosé and M.L. Klein, “Constant pressure molecular dynamics for molecular systems,” Mol. Phys., 50 1055–1076 (1983).

⁴⁰ G. Liu, “Dynamical equations for the period vectors in a periodic system under constant external stress,” Can. J. Phys., 93 974–978 (2015).

⁴¹ M.E. Tuckerman, J. Alejandre, R. López-Rendón, A.L. Jochim, and G.J. Martyna, “A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal-isobaric ensemble,” J. Phys. A., 59 5629–5651 (2006).

⁴² T.-Q. Yu, J. Alejandre, R. Lopez-Rendon, G.J. Martyna, and M.E. Tuckerman, “Measure-preserving integrators for molecular dynamics in the isothermal-isobaric ensemble derived from the liouville operator,” Chem. Phys., 370 294–305 (2010).

⁴³ B.G. Dick and A.W. Overhauser, “Theory of the dielectric constants of alkali halide crystals,” Phys. Rev., 112 90–103 (1958).

⁴⁴ P.C. Jordan, P.J. van Maaren, J. Mavri, D. van der Spoel, and H.J.C. Berendsen, “Towards phase transferable potential functions: Methodology and application to nitrogen,” J. Chem. Phys., 103 2272–2285 (1995).

⁴⁵ P.J. van Maaren and D. van der Spoel, “Molecular dynamics simulations of a water with a novel shell-model potential,” J. Phys. Chem. B., 105 2618–2626 (2001).

⁴⁶ J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen, “Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes,” J. Comp. Phys., 23 327–341 (1977).

⁴⁷ S. Miyamoto and P.A. Kollman, “SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models,” J. Comp. Chem., 13 952–962 (1992).

⁴⁸ H.C. Andersen, “RATTLE: A ‘Velocity’ version of the SHAKE algorithm for molecular dynamics calculations,” J. Comp. Phys., 52 24–34 (1983).

⁴⁹ B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije, “LINCS: A linear constraint solver for molecular simulations,” J. Comp. Chem., 18 1463–1472 (1997).

⁵⁰ B. Hess, “P-LINCS: A parallel linear constraint solver for molecular simulation,” J. Chem. Theory Comput., 4 116–122 (2007).

⁵¹ N. Goga, A.J. Rzepiela, A.H. de Vries, S.J. Marrink, and H.J.C. Berendsen, “Efficient algorithms for Langevin and DPD dynamics,” J. Chem. Theory Comput., 8 3637–3649 (2012).

⁵² R.H. Byrd, P. Lu, and J. Nocedal, “A limited memory algorithm for bound constrained optimization,” SIAM J. Scientif. Statistic. Comput., 16 1190–1208 (1995).

⁵³ C. Zhu, R.H. Byrd, and J. Nocedal, “L-BFGS-B: Algorithm 778: L-BFGS-B, FORTRAN routines for large scale bound constrained optimization,” ACM Trans. Math. Softw., 23 550–560 (1997).

⁵⁴ M. Levitt, C. Sander, and P.S. Stern, “The normal modes of a protein: Native bovine pancreatic trypsin inhibitor,” Int. J. Quant. Chem: Quant. Biol. Symp., 10 181–199 (1983).

⁵⁵ N. G\(\bar{\rm o}\), T. Noguti, and T. Nishikawa, “Dynamics of a small globular protein in terms of low-frequency vibrational modes,” Proc. Natl. Acad. Sci. USA, 80 3696–3700 (1983).

⁵⁶ B. Brooks and M. Karplus, “Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor,” Proc. Natl. Acad. Sci. USA, 80 6571–6575 (1983).

⁵⁷ S. Hayward and N. G\(\bar{\rm o}\), “Collective variable description of native protein dynamics,” Annu. Rev. Phys. Chem., 46 223–250 (1995).

⁵⁸ C.H. Bennett, “Efficient Estimation of Free Energy Differences from Monte Carlo Data,” J. Comp. Phys., 22 245–268 (1976).

⁵⁹ M.R. Shirts and J.D. Chodera, “Statistically optimal analysis of multiple equilibrium simulations,” J. Chem. Phys., 129 124105 (2008).

⁶⁰ K. Hukushima and K. Nemoto, “Exchange Monte Carlo Method and Application to Spin Glass Simulations,” J. Phys. Soc. Jpn., 65 1604–1608 (1996).

⁶¹ Y. Sugita and Y. Okamoto, “Replica-exchange molecular dynamics method for protein folding,” Chem. Phys. Lett., 314 141–151 (1999).

⁶² M. Seibert, A. Patriksson, B. Hess, and D. van der Spoel, “Reproducible polypeptide folding and structure prediction using molecular dynamics simulations,” J. Mol. Biol., 354 173–183 (2005).

⁶³ T. Okabe, M. Kawata, Y. Okamoto, and M. Mikami, “Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble,” Chem. Phys. Lett., 335 435–439 (2001).

⁶⁴ J.D. Chodera and M.R. Shirts, “Replica exchange and expanded ensemble simulations as gibbs sampling: Simple improvements for enhanced mixing,” J. Chem. Phys., 135 194110 (2011).

⁶⁵ B.L. de Groot, A. Amadei, D.M.F. van Aalten, and H.J.C. Berendsen, “Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin,” J. Biomol. Str. Dyn., 13 [5] 741–751 (1996).

⁶⁶ B.L. de Groot, A. Amadei, R.M. Scheek, N.A.J. van Nuland, and H.J.C. Berendsen, “An extended sampling of the configurational space of HPr from E. coli,” PROTEINS: Struct. Funct. Gen., 26 314–322 (1996).

⁶⁷ O.E. Lange, L.V. Schafer, and H. Grubmuller, “Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics,” J. Comp. Chem., 27 1693–1702 (2006).

⁶⁸ A.P. Lyubartsev, A.A. Martsinovski, S.V. Shevkunov, and P.N. Vorontsov-Velyaminov, “New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles,” J. Chem. Phys., 96 1776–1783 (1992).

⁶⁹ S.Y. Liem, D. Brown, and J.H.R. Clarke, “Molecular dynamics simulations on distributed memory machines,” Comput. Phys. Commun., 67 [2] 261–267 (1991).

⁷⁰ K.J. Bowers, R.O. Dror, and D.E. Shaw, “The midpoint method for parallelization of particle simulations,” J. Chem. Phys., 124 [18] 184109–184109 (2006).

⁷² D. van der Spoel and P.J. van Maaren, “The origin of layer structure artifacts in simulations of liquid water,” J. Chem. Theory Comput., 2 1–11 (2006).

⁷³ I. Ohmine, H. Tanaka, and P.G. Wolynes, “Large local energy fluctuations in water. II. Cooperative motions and fluctuations,” J. Chem. Phys., 89 5852–5860 (1988).

⁷⁴ D.B. Kitchen, F. Hirata, J.D. Westbrook, R. Levy, D. Kofke, and M. Yarmush, “Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water,” J. Comp. Chem., 11 1169–1180 (1990).

⁷⁵ J. Guenot and P.A. Kollman, “Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation,” J. Comp. Chem., 14 295–311 (1993).

⁷⁶ P.J. Steinbach and B.R. Brooks, “New spherical-cutoff methods for long-range forces in macromolecular simulation,” J. Comp. Chem., 15 667–683 (1994).

⁷⁷ W.F. van Gunsteren, S.R. Billeter, A.A. Eising, P.H. Hünenberger, P. Krüger, A.E. Mark, W.R.P. Scott, and I.G. Tironi, Biomolecular simulation: The GROMOS96 manual and user guide. Hochschulverlag AG an der ETH Zürich, Zürich, Switzerland, 1996.

⁷⁸ W.F. van Gunsteren and H.J.C. Berendsen, Gromos-87 manual. Biomos BV, Nijenborgh 4, 9747 AG Groningen, The Netherlands, 1987.

⁷⁹ P.M. Morse, “Diatomic molecules according to the wave mechanics. II. vibrational levels.” Phys. Rev., 34 57–64 (1929).

⁸⁰ H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans, “Interaction models for water in relation to protein hydration”; pp. 331–342 in Intermolecular forces. Edited by B. Pullman. D. Reidel Publishing Company, Dordrecht, 1981.

⁸¹ D.M. Ferguson, “Parametrization and evaluation of a flexible water model,” J. Comp. Chem., 16 501–511 (1995).

⁸² H.R. Warner Jr., “Kinetic theory and rheology of dilute suspensions of finitely extendible dumbbells,” Ind. Eng. Chem. Fundam., 11 [3] 379–387 (1972).

⁸³ M. Bulacu, N. Goga, W. Zhao, G. Rossi, L. Monticelli, X. Periole, D. Tieleman, and S. Marrink, “Improved angle potentials for coarse-grained molecular dynamics simulations,” J. Chem. Theory Comput., 9 [8] 3282-3292 (2013).

⁸⁴ 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 calculation,” J. Comp. Chem., 4 187–217 (1983).

⁸⁵ C.P. Lawrence and J.L. Skinner, “Flexible TIP4P model for molecular dynamics simulation of liquid water,” Chem. Phys. Lett., 372 842–847 (2003).

⁸⁶ W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives, “Development and testing of the oPLS all-atom force field on conformational energetics and properties of organic liquids,” J. Am. Chem. Soc., 118 11225–11236 (1996).

⁸⁷ M.J. Robertson, J. Tirado-Rives, and W.L. Jorgensen, “Improved peptide and protein torsional energetics with the oPLS-aA force field,” J. Chem. Theory Comput., 11 3499–3509 (2015).

⁸⁸ M. Bulacu and E. van der Giessen, “Effect of bending and torsion rigidity on self-diffusion in polymer melts: A molecular-dynamics study,” J. Chem. Phys., 123 [11] 114901 (2005).

⁸⁹ R.A. Scott and H. Scheraga, “Conformational analysis of macromolecules,” J. Chem. Phys., 44 3054–3069 (1966).

⁹⁰ L. Pauling, The nature of chemical bond. Cornell University Press, Ithaca; New York, 1960.

⁹¹ A.E. Torda, R.M. Scheek, and W.F. van Gunsteren, “Time-dependent distance restraints in molecular dynamics simulations,” Chem. Phys. Lett., 157 289–294 (1989).

⁹² B. Hess and R.M. Scheek, “Orientation restraints in molecular dynamics simulations using time and ensemble averaging,” J. Magn. Reson., 164 19–27 (2003).

⁹³ P.E.M. Lopes, J. Huang, J. Shim, Y. Luo, H. Li, B. Roux, and J. MacKerell Alexander D., “Polarizable force field for peptides and proteins based on the classical drude oscillator,” J. Chem. Theory Comput, 9 5430–5449 (2013).

⁹⁴ H. Yu, T.W. Whitfield, E. Harder, G. Lamoureux, I. Vorobyov, V.M. Anisimov, A.D. MacKerell, Jr., and B. Roux, “Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field,” J. Chem. Theory Comput., 6 774–786 (2010).

⁹⁵ B.T. Thole, “Molecular polarizabilities with a modified dipole interaction,” Chem. Phys., 59 341–345 (1981).

⁹⁶ G. Lamoureux and B. Roux, “Modeling induced polarization with classical drude oscillators: Theory and molecular dynamics simulation algorithm,” J. Chem. Phys., 119 3025–3039 (2003).

⁹⁷ G. Lamoureux, A.D. MacKerell, and B. Roux, “A simple polarizable model of water based on classical drude oscillators,” J. Chem. Phys., 119 5185–5197 (2003).

⁹⁸ S.Y. Noskov, G. Lamoureux, and B. Roux, “Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field,” J. Phys. Chem. B., 109 6705–6713 (2005).

⁹⁹ W.F. van Gunsteren and A.E. Mark, “Validation of molecular dynamics simulations,” J. Chem. Phys., 108 6109–6116 (1998).

¹⁰⁰ T.C. Beutler, A.E. Mark, R.C. van Schaik, P.R. Greber, 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).

¹⁰³ W.L. Jorgensen and J. Tirado-Rives, “The OPLS potential functions for proteins. energy minimizations for crystals of cyclic peptides and crambin,” J. Am. Chem. Soc., 110 1657–1666 (1988).

¹⁰⁴ H.J.C. Berendsen and W.F. van Gunsteren, “Molecular dynamics simulations: Techniques and approaches”; pp. 475–500 in Molecular liquids-dynamics and interactions. Edited by A.J.B. et al. Reidel, Dordrecht, The Netherlands, 1984.

¹⁰⁵ P.P. Ewald, “Die Berechnung optischer und elektrostatischer Gitterpotentiale,” Ann. Phys., 64 253–287 (1921).

¹⁰⁶ R.W. Hockney and J.W. Eastwood, Computer simulation using particles. McGraw-Hill, New York, 1981.

¹⁰⁷ V. Ballenegger, J.J. Cerdà, and C. Holm, “How to convert SPME to P3M: Influence functions and error estimates,” J. Chem. Theory Comput., 8 [3] 936–947 (2012).

¹⁰⁸ M.P. Allen and D.J. Tildesley, Computer simulations of liquids. Oxford Science Publications, Oxford, 1987.

¹⁰⁹ C.L. Wennberg, T. Murtola, B. Hess, and E. Lindahl, “Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties,” J. Chem. Theory Comput., 9 3527–3537 (2013).

¹¹⁰ C. Oostenbrink, A. Villa, A.E. Mark, and W.F. Van Gunsteren, “A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6,” Journal of Computational Chemistry, 25 [13] 1656–1676 (2004).

¹¹¹ W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.R. Merz Jr., D.M. Ferguson, D.C. Spellmeyer, and T. Fox et al., “A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules,” J. Am. Chem. Soc., 117 [19] 5179–5197 (1995).

¹¹² P.A. Kollman, “Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules,” Acc. Chem. Res., 29 [10] 461–469 (1996).

¹¹³ J. Wang, P. Cieplak, and P.A. Kollman, “How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules?” J. Comp. Chem., 21 [12] 1049–1074 (2000).

¹¹⁴ V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling, “Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters,” PROTEINS: Struct. Funct. Gen., 65 712–725 (2006).

¹¹⁵ K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J.L. Klepeis, R.O. Dorr, and D.E. Shaw, “Improved side-chain torsion potentials for the AMBER ff99SB protein force field,” PROTEINS: Struct. Funct. Gen., 78 1950–1958 (2010).

¹¹⁶ Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, G. Xiong, W. Zhang, R. Yang, and P. Cieplak et al., “A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations,” J. Comp. Chem., 24 [16] 1999–2012 (2003).

¹¹⁷ A.E. García and K.Y. Sanbonmatsu, “\(\alpha\)-Helical stabilization by side chain shielding of backbone hydrogen bonds,” Proc. Natl. Acad. Sci. USA, 99 [5] 2782–2787 (2002).

¹¹⁸ J. MacKerell A. D., M. Feig, and C.L. Brooks III, “Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations,” J. Comp. Chem., 25 [11] 1400–15 (2004).

¹¹⁹ A.D. MacKerell, D. Bashford, Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, and J. Gao et al., “All-atom empirical potential for molecular modeling and dynamics studies of proteins,” J. Phys. Chem. B., 102 [18] 3586–3616 (1998).

¹²⁰ S.E. Feller and A.D. MacKerell, “An improved empirical potential energy function for molecular simulations of phospholipids,” J. Phys. Chem. B., 104 [31] 7510–7515 (2000).

¹²¹ N. Foloppe and A.D. MacKerell, “All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data,” J. Comp. Chem., 21 [2] 86–104 (2000).

¹²² A.D. MacKerell and N.K. Banavali, “All-atom empirical force field for nucleic acids: II. application to molecular dynamics simulations of DNA and RNA in solution,” J. Comp. Chem., 21 [2] 105–120 (2000).

¹²³ P. Larsson and E. Lindahl, “A High-Performance Parallel-Generalized Born Implementation Enabled by Tabulated Interaction Rescaling,” J. Comp. Chem., 31 [14] 2593–2600 (2010).

¹²⁴ P. Bjelkmar, P. Larsson, M.A. Cuendet, B. Hess, and E. Lindahl, “Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models,” J. Chem. Theory Comput., 6 459–466 (2010).

¹²⁵ A. Kohlmeyer and J. Vermaas, TopoTools: Release 1.6 with CHARMM export in topogromacs, (2016).

¹²⁶ T. Bereau, Z.-J. Wang, and M. Deserno, Solvent-free coarse-grained model for unbiased high-resolution protein-lipid interactions, (n.d.).

¹²⁷ Z.-J. Wang and M. Deserno, “A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations,” J. Phys. Chem. B., 114 [34] 11207–11220 (2010).

¹²⁸ W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein, “Comparison of simple potential functions for simulating liquid water,” J. Chem. Phys., 79 926–935 (1983).

¹²⁹ IUPAC-IUB Commission on Biochemical Nomenclature, “Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains. Tentative Rules (1969),” Biochemistry, 9 3471–3478 (1970).

¹³⁰ M.W. Mahoney and W.L. Jorgensen, “A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions,” J. Chem. Phys., 112 8910–8922 (2000).

¹³¹ J.P. Ryckaert and A. Bellemans, “Molecular dynamics of liquid alkanes,” Far. Disc. Chem. Soc., 66 95–106 (1978).

¹³² H. de Loof, L. Nilsson, and R. Rigler, “Molecular dynamics simulations of galanin in aqueous and nonaqueous solution,” J. Am. Chem. Soc., 114 4028–4035 (1992).

¹³³ A.R. van Buuren and H.J.C. Berendsen, “Molecular Dynamics simulation of the stability of a 22 residue alpha-helix in water and 30% trifluoroethanol,” Biopolymers, 33 1159–1166 (1993).

¹³⁴ R.M. Neumann, “Entropic approach to Brownian Movement,” Am. J. Phys., 48 354–357 (1980).

¹³⁵ C. Jarzynski, “Nonequilibrium equality for free energy differences,” Phys. Rev. Lett., 78 [14] 2690–2693 ().

¹³⁶ M.S. O. Engin A. Villa and B. Hess, “Driving forces for adsorption of amphiphilic peptides to air-water interface,” J. Phys. Chem. B., (2010).

¹³⁷ V. Lindahl, J. Lidmar, and B. Hess, “Accelerated weight histogram method for exploring free energy landscapes,” The Journal of chemical physics, 141 [4] 044110 (2014).

¹³⁸ F. Wang and D. Landau, “Efficient, multiple-range random walk algorithm to calculate the density of states,” Physical review letters, 86 [10] 2050 (2001).

¹³⁹ T. Huber, A.E. Torda, and W.F. 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 (1994).

¹⁴⁰ A. Laio and M. Parrinello, “Escaping free-energy minima,” Proceedings of the National Academy of Sciences, 99 [20] 12562–12566 (2002).

¹⁴¹ R. Belardinelli and V. Pereyra, “Fast algorithm to calculate density of states,” Physical Review E, 75 [4] 046701 (2007).

¹⁴² A. Barducci, G. Bussi, and M. Parrinello, “Well-tempered metadynamics: A smoothly converging and tunable free-energy method,” Physical review letters, 100 [2] 020603 (2008).

¹⁴³ V. Lindahl, A. Villa, and B. Hess, “Sequence dependency of canonical base pair opening in the dNA double helix,” PLoS computational biology, 13 [4] e1005463 (2017).

¹⁴⁴ D.A. Sivak and G.E. Crooks, “Thermodynamic metrics and optimal paths,” Physical review letters, 108 [19] 190602 (2012).

¹⁴⁵ C. Kutzner, J. Czub, and H. Grubmüller, “Keep it flexible: Driving macromolecular rotary motions in atomistic simulations with GROMACS,” J. Chem. Theory Comput., 7 1381–1393 (2011).

¹⁴⁶ C. Caleman and D. van der Spoel, “Picosecond Melting of Ice by an Infrared Laser Pulse - A simulation study,” Angew. Chem., Int. Ed. Engl., 47 1417–1420 (2008).

¹⁴⁷ C. Kutzner, H. Grubmüller, B.L. de Groot, and U. Zachariae, “Computational electrophysiology: The molecular dynamics of ion channel permeation and selectivity in atomistic detail,” Biophys. J., 101 809–817 (2011).

¹⁴⁸ K.A. Feenstra, B. Hess, and H.J.C. Berendsen, “Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems,” J. Comp. Chem., 20 786–798 (1999).

¹⁴⁹ B. Hess, “Determining the shear viscosity of model liquids from molecular dynamics,” J. Chem. Phys., 116 209–217 (2002).

¹⁵⁰ M.J.S. Dewar, “Development and status of MINDO/3 and MNDO,” J. Mol. Struct., 100 41 (1983).

¹⁵¹ M.F. Guest, R.J. Harrison, J.H. van Lenthe, and L.C.H. van Corler, “Computational chemistry on the FPS-X64 scientific computers - Experience on single- and multi-processor systems,” Theor. Chim. Act., 71 117 (1987).

¹⁵² M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery Jr., and T. Vreven et al., Gaussian 03, Revision C.02, (n.d.).

¹⁵³ R. Car and M. Parrinello, “Unified approach for molecular dynamics and density-functional theory,” Phys. Rev. Lett., 55 2471–2474 (1985).

¹⁵⁴ M. Field, P.A. Bash, and M. Karplus, “A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulation,” J. Comp. Chem., 11 700 (1990).

¹⁵⁵ F. Maseras and K. Morokuma, “IMOMM: A New Ab Initio + Molecular Mechanics Geometry Optimization Scheme of Equilibrium Structures and Transition States,” J. Comp. Chem., 16 1170–1179 (1995).

¹⁵⁶ M. Svensson, S. Humbel, R.D.J. Froes, T. Matsubara, S. Sieber, and K. Morokuma, “ONIOM a multilayered integrated MO + MM method for geometry optimizations and single point energy predictions. a test for Diels-Alder reactions and Pt(P(t-Bu)3)2 + H2 oxidative addition,” J. Phys. Chem., 100 19357 (1996).

¹⁵⁷ S. Yesylevskyy, “ProtSqueeze: Simple and effective automated tool for setting up membrane protein simulations,” J. Chem. Inf. Model., 47 1986–1994 (2007).

¹⁵⁸ M. Wolf, M. Hoefling, C. Aponte-Santamaría, H. Grubmüller, and G. Groenhof, “g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation,” J. Comp. Chem., 31 2169–2174 (2010).

¹⁵⁹ D. van der Spoel and H.J.C. Berendsen, “Molecular dynamics simulations of Leu-enkephalin in water and DMSO,” Biophys. J., 72 2032–2041 (1997).

¹⁶⁰ P.E. Smith and W.F. van Gunsteren, “The Viscosity of SPC and SPC/E Water,” Chem. Phys. Lett., 215 315–318 (1993).

¹⁶¹ S. Balasubramanian, C.J. Mundy, and M.L. Klein, “Shear viscosity of polar fluids: Molecular dynamics calculations of water,” J. Chem. Phys., 105 11190–11195 (1996).

¹⁶² J. Wuttke, Lmfit, (2013).

¹⁶³ B. Steen-Sæthre, A.C. Hoffmann, and D. van der Spoel, “Order parameters and algorithmic approaches for detection and demarcation of interfaces in hydrate-fluid and ice-fluid systems,” J. Chem. Theor. Comput., 10 5606–5615 (2014).

¹⁶⁴ B.J. Palmer, “Transverse-current autocorrelation-function calculations of the shear viscosity for molecular liquids.” Phys. Rev. E, 49 359–366 (1994).

¹⁶⁵ E.J.W. Wensink, A.C. Hoffmann, P.J. van Maaren, and D. van der Spoel, “Dynamic properties of water/alcohol mixtures studied by computer simulation,” J. Chem. Phys., 119 7308–7317 (2003).

¹⁶⁶ G.-J. Guo, Y.-G. Zhang, K. Refson, and Y.-J. Zhao, “Viscosity and stress autocorrelation function in supercooled water: A molecular dynamics study,” Mol. Phys., 100 2617–2627 (2002).

¹⁶⁷ G.S. Fanourgakis, J.S. Medina, and R. Prosmiti, “Determining the bulk viscosity of rigid water models,” J. Phys. Chem. A, 116 2564–2570 (2012).

¹⁶⁸ D. van der Spoel, H.J. Vogel, and H.J.C. Berendsen, “Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein,” PROTEINS: Struct. Funct. Gen., 24 450–466 (1996).

¹⁶⁹ A. Amadei, A.B.M. Linssen, and H.J.C. Berendsen, “Essential dynamics of proteins,” PROTEINS: Struct. Funct. Gen., 17 412–425 (1993).

¹⁷⁰ B. Hess, “Convergence of sampling in protein simulations,” Phys. Rev. **E**, 65 031910 (2002).

¹⁷¹ B. Hess, “Similarities between principal components of protein dynamics and random diffusion,” Phys. Rev. **E**, 62 8438–8448 (2000).

¹⁷² Y. Mu, P.H. Nguyen, and G. Stock, “Energy landscape of a small peptide revealed by dihedral angle principal component analysis,” PROTEINS: Struct. Funct. Gen., 58 45–52 (2005).

¹⁷³ D. van der Spoel, P.J. van Maaren, P. Larsson, and N. Timneanu, “Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media,” J. Phys. Chem. B., 110 4393–4398 (2006).

¹⁷⁴ A. Luzar and D. Chandler, “Hydrogen-bond kinetics in liquid water,” Nature, 379 55–57 (1996).

¹⁷⁵ A. Luzar, “Resolving the hydrogen bond dynamics conundrum,” J. Chem. Phys., 113 10663–10675 (2000).

¹⁷⁶ W. Kabsch and C. Sander, “Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features,” Biopolymers, 22 2577–2637 (1983).

¹⁷⁷ H. Bekker, H.J.C. Berendsen, E.J. Dijkstra, S. Achterop, R. v. Drunen, D. v. d. Spoel, A. Sijbers, and H. Keegstra et al., “Gromacs Method of Virial Calculation Using a Single Sum”; pp. 257–261 in Physics computing 92. Edited by R.A. de Groot and J. Nadrchal. World Scientific, Singapore, 1993.

¹⁷⁸ H.J.C. Berendsen, J.R. Grigera, and T.P. Straatsma, “The missing term in effective pair potentials,” J. Phys. Chem., 91 6269–6271 (1987).

¹⁷⁹ W.F. van Gunsteren and H.J.C. Berendsen, Molecular dynamics of simple systems, (1994).

¹⁸⁰ A. Laio, J. VandeVondele, U. Rothlisberger, A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations, (2002).

¹⁸¹ Hub, J. S., de Groot, B. L., Grubmüller, H., Groenhof, G., “Quantifying artifacts in Ewald simulations of inhomogeneous systems with a net charge,” J. Chem. Theory Comput., 10, 381–390 (2014).

¹⁸² Páll, S., Hess, B., “A flexible algorithm for calculating pair interactions on SIMD architectures,” Comput. Phys. Commun., 183, 2641–2650 (2013).

¹⁸³ V. Gapsys, D. Seeliger, and B.L. de Groot, “New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations”, J. Chem. Theor. Comput., 8 2373-2382 (2012).

¹⁸⁴ Bernetti, M. and Bussi G., “Pressure control using stochastic cell rescaling”, J. Chem. Phys., 153, 114107 (2020).

¹⁸⁵ Lidmar J., “Improving the efficiency of extended ensemble simulations: The accelerated weight histogram method”, Phys. Rev. E, 85, 0256708 (2012).

¹⁸⁶ Lindahl V., Lidmar J. and Hess B., “Riemann metric approach to optimal sampling of multidimensional free-energy landscapes”, Phys. Rev. E, 98, 023312 (2018).

¹⁸⁷ Lundborg M., Lidmar J. and Hess B., “The accelerated weight histogram method for alchemical free energy calculations”, J. Chem. Phys., 154, 204103 (2021).

¹⁸⁸ Kühne T., Iannuzzi M., Del Ben M. and Hutter J. et al., “CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations”, J. Chem. Phys., 152, 194103 (2020).

¹⁸⁹ Laino T., Mohamed F., Laio A. and Parrinello M., “An Efficient Real Space Multigrid QM/MM Electrostatic Coupling”, J. Chem. Theory Comput., 1, 1176 (2005).

¹⁹⁰ D. van der Spoel, H. Henschel, P. J. van Maaren, M. M. Ghahremanpour , and L. T. Costa, “A potential for molecular simulation of compounds with linear moieties”, J. Chem. Phys., 153 084503 (2020).

¹⁹¹ M. Tuckerman, B. J. Berne, and G. J. Martyna, “Reversible multiple time scale molecular dynamics”, J. Chem. Phys., 97 1990 (1992).

¹⁹² Orzechowski M, Tama F., “Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations”, Biophysical journal, 95, 5692–705, (2008).

¹⁹³ Igaev, M., Kutzner, C., Bock, L. V., Vaiana, A. C., & Grubmüller, H., “Automated cryo-EM structure refinement using correlation-driven molecular dynamics”, eLife, 8, e43542 (2019).

¹⁹⁴ Lundborg M., Lidmar J. and Hess B., “On the Path to Optimal Alchemistry”, Protein J., 42, 477–489 (2023).

¹⁹⁵ G. Fiorin, M. L. Klein, and J. Hénin, “Using collective variables to drive molecular dynamics simulations”, Mol. Phys. 111 3345-3362 (2013).