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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).

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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).

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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).