8 <div id="refs" class="references">
12 <div id="ref-Bekker93a">
16 :sup:`1` H. Bekker, H.J.C. Berendsen, E.J. Dijkstra, S. Achterop, R. van
17 Drunen, D. van der Spoel, A. Sijbers, and H. Keegstra *et al.*, "Gromacs: A parallel computer for molecular dynamics simulations";
18 pp. 252–256 in *Physics computing 92*. Edited by R.A. de Groot and J.
19 Nadrchal. World Scientific, Singapore, 1993.
27 <div id="ref-Berendsen95a">
31 :sup:`2` H.J.C. Berendsen, D. van der Spoel, and R. van Drunen,
32 "GROMACS: A message-passing parallel molecular dynamics implementation,"
33 *Comp. Phys. Comm.*, **91** 43–56 (1995).
41 <div id="ref-Lindahl2001a">
45 :sup:`3` E. Lindahl, B. Hess, and D. van der Spoel, "GROMACS 3.0: A
46 package for molecular simulation and trajectory analysis," *J. Mol.
47 Mod.*, **7** 306–317 (2001).
55 <div id="ref-Spoel2005a">
59 :sup:`4` D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark,
60 and H.J.C. Berendsen, "GROMACS: Fast, Flexible and Free," *J. Comp.
61 Chem.*, **26** 1701–1718 (2005).
69 <div id="ref-Hess2008b">
73 :sup:`5` B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, "GROMACS
74 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable
75 Molecular Simulation," *J. Chem. Theory Comput.*, **4** [3] 435–447
84 <div id="ref-Pronk2013">
88 :sup:`6` S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R.
89 Apostolov, M.R. Shirts, and J.C. Smith *et al.*, "GROMACS 4.5: A
90 high-throughput and highly parallel open source molecular simulation
91 toolkit," *Bioinformatics*, **29** [7] 845–854 (2013).
99 <div id="ref-Pall2015">
103 :sup:`7` S. Páll, M.J. Abraham, C. Kutzner, B. Hess, and E. Lindahl,
104 "Tackling exascale software challenges in molecular dynamics simulations
105 with GROMACS"; pp. 3–27 in *Solving software challenges for exascale*.
106 Edited by S. Markidis and E. Laure. Springer International Publishing
107 Switzerland, London, 2015.
115 <div id="ref-Abraham2015">
119 :sup:`8` M.J. Abraham, T. Murtola, R. Schulz, S. Páll, J.C. Smith, B.
120 Hess, and E. Lindahl, "GROMACS: High performance molecular simulations
121 through multi-level parallelism from laptops to supercomputers,"
122 *SoftwareX*, **1–2** 19–25 (2015).
130 <div id="ref-Gunsteren90">
134 :sup:`9` W.F. van Gunsteren and H.J.C. Berendsen, "Computer simulation
135 of molecular dynamics: Methodology, applications, and perspectives in
136 chemistry," *Angew. Chem. Int. Ed. Engl.*, **29** 992–1023 (1990).
144 <div id="ref-Fraaije93">
148 :sup:`10` J.G.E.M. Fraaije, "Dynamic density functional theory for
149 microphase separation kinetics of block copolymer melts," *J. Chem.
150 Phys.*, **99** 9202–9212 (1993).
158 <div id="ref-McQuarrie76">
162 :sup:`11` D.A. McQuarrie, *Statistical mechanics*. Harper & Row, New
171 <div id="ref-Gunsteren77">
175 :sup:`12` W.F. van Gunsteren and H.J.C. Berendsen, "Algorithms for
176 macromolecular dynamics and constraint dynamics," *Mol. Phys.*, **34**
185 <div id="ref-Gunsteren82">
189 :sup:`13` W.F. van Gunsteren and M. Karplus, "Effect of constraints on
190 the dynamics of macromolecules," *Macromolecules*, **15** 1528–1544
199 <div id="ref-Darden93">
203 :sup:`14` T. Darden, D. York, and L. Pedersen, "Particle mesh Ewald: An
204 N\ :math:`\bullet`\ log(N) method for Ewald sums in large systems," *J.
205 Chem. Phys.*, **98** 10089–10092 (1993).
213 <div id="ref-Essmann95">
217 :sup:`15` U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and
218 L.G. Pedersen, "A smooth particle mesh ewald potential," *J. Chem.
219 Phys.*, **103** 8577–8592 (1995).
227 <div id="ref-Geman84">
231 :sup:`16` S. Geman and D. Geman, "Stochastic relaxation, Gibbs
232 distributions and the Bayesian restoration of images," *IEEE Trans.
233 Patt. Anal. Mach. Int.*, **6** 721 (1984).
241 <div id="ref-Nilges88">
245 :sup:`17` M. Nilges, G.M. Clore, and A.M. Gronenborn, "Determination of
246 three-dimensional structures of proteins from interproton distance data
247 by dynamical simulated annealing from a random array of atoms," *FEBS
248 Lett.*, **239** 129–136 (1988).
256 <div id="ref-Schaik93">
260 :sup:`18` R.C. van Schaik, H.J.C. Berendsen, A.E. Torda, and W.F. van
261 Gunsteren, "A structure refinement method based on molecular dynamics in
262 4 spatial dimensions," *J. Mol. Biol.*, **234** 751–762 (1993).
270 <div id="ref-Zimmerman91">
274 :sup:`19` K. Zimmerman, "All purpose molecular mechanics simulator and
275 energy minimizer," *J. Comp. Chem.*, **12** 310–319 (1991).
283 <div id="ref-Adams79">
287 :sup:`20` D.J. Adams, E.M. Adams, and G.J. Hills, "The computer
288 simulation of polar liquids," *Mol. Phys.*, **38** 387–400 (1979).
296 <div id="ref-Bekker95">
300 :sup:`21` H. Bekker, E.J. Dijkstra, M.K.R. Renardus, and H.J.C.
301 Berendsen, "An efficient, box shape independent non-bonded force and
302 virial algorithm for molecular dynamics," *Mol. Sim.*, **14** 137–152
311 <div id="ref-Hockney74">
315 :sup:`22` R.W. Hockney, S.P. Goel, and J. Eastwood, "Quiet High
316 Resolution Computer Models of a Plasma," *J. Comp. Phys.*, **14**
325 <div id="ref-Verlet67">
329 :sup:`23` L. Verlet., "Computer experiments on classical fluids. I.
330 Thermodynamical properties of Lennard-Jones molecules," *Phys. Rev.*,
331 **159** 98–103 (1967).
339 <div id="ref-Berendsen86b">
343 :sup:`24` H.J.C. Berendsen and W.F. van Gunsteren, "Practical algorithms
344 for dynamics simulations"; in 1986.
352 <div id="ref-Swope82">
356 :sup:`25` W.C. Swope, H.C. Andersen, P.H. Berens, and K.R. Wilson, "A
357 computer-simulation method for the calculation of equilibrium-constants
358 for the formation of physical clusters of molecules: Application to
359 small water clusters," *J. Chem. Phys.*, **76** 637–649 (1982).
367 <div id="ref-Berendsen84">
371 :sup:`26` H.J.C. Berendsen, J.P.M. Postma, A. DiNola, and J.R. Haak,
372 "Molecular dynamics with coupling to an external bath," *J. Chem.
373 Phys.*, **81** 3684–3690 (1984).
381 <div id="ref-Andersen80">
385 :sup:`27` H.C. Andersen, "Molecular dynamics simulations at constant
386 pressure and/or temperature," *J. Chem. Phys.*, **72** 2384 (1980).
394 <div id="ref-Nose84">
398 :sup:`28` S. Nosé, "A molecular dynamics method for simulations in the
399 canonical ensemble," *Mol. Phys.*, **52** 255–268 (1984).
407 <div id="ref-Hoover85">
411 :sup:`29` W.G. Hoover, "Canonical dynamics: Equilibrium phase-space
412 distributions," *Phys. Rev. **A***, **31** 1695–1697 (1985).
420 <div id="ref-Bussi2007a">
424 :sup:`30` G. Bussi, D. Donadio, and M. Parrinello, "Canonical sampling
425 through velocity rescaling," *J. Chem. Phys.*, **126** 014101 (2007).
433 <div id="ref-Berendsen91">
437 :sup:`31` H.J.C. Berendsen, "Transport properties computed by linear
438 response through weak coupling to a bath"; pp. 139–155 in *Computer
439 simulations in material science*. Edited by M. Meyer and V. Pontikis.
448 <div id="ref-Basconi2013">
452 :sup:`32` J.E. Basconi and M.R. Shirts, "Effects of temperature control
453 algorithms on transport properties and kinetics in molecular dynamics
454 simulations," *J. Chem. Theory Comput.*, **9** [7] 2887–2899 (2013).
462 <div id="ref-Cooke2008">
466 :sup:`33` B. Cooke and S.J. Schmidler, "Preserving the Boltzmann
467 ensemble in replica-exchange molecular dynamics," *J. Chem. Phys.*,
468 **129** 164112 (2008).
476 <div id="ref-Martyna1992">
480 :sup:`34` G.J. Martyna, M.L. Klein, and M.E. Tuckerman, "Nosé-Hoover
481 chains: The canonical ensemble via continuous dynamics," *J. Chem.
482 Phys.*, **97** 2635–2643 (1992).
490 <div id="ref-Martyna1996">
494 :sup:`35` G.J. Martyna, M.E. Tuckerman, D.J. Tobias, and M.L. Klein,
495 "Explicit reversible integrators for extended systems dynamics," *Mol.
496 Phys.*, **87** 1117–1157 (1996).
504 <div id="ref-Holian95">
508 :sup:`36` B.L. Holian, A.F. Voter, and R. Ravelo, "Thermostatted
509 molecular dynamics: How to avoid the Toda demon hidden in Nosé-Hoover
510 dynamics," *Phys. Rev. E*, **52** [3] 2338–2347 (1995).
518 <div id="ref-Eastwood2010">
522 :sup:`37` M.P. Eastwood, K.A. Stafford, R.A. Lippert, M.Ø. Jensen, P.
523 Maragakis, C. Predescu, R.O. Dror, and D.E. Shaw, "Equipartition and the
524 calculation of temperature in biomolecular simulations," *J. Chem.
525 Theory Comput.*, **ASAP** DOI: 10.1021/ct9002916 (2010).
533 <div id="ref-Parrinello81">
537 :sup:`38` M. Parrinello and A. Rahman, "Polymorphic transitions in
538 single crystals: A new molecular dynamics method," *J. Appl. Phys.*,
539 **52** 7182–7190 (1981).
547 <div id="ref-Nose83">
551 :sup:`39` S. Nosé and M.L. Klein, "Constant pressure molecular dynamics
552 for molecular systems," *Mol. Phys.*, **50** 1055–1076 (1983).
560 <div id="ref-Liu2015">
564 :sup:`40` G. Liu, "Dynamical equations for the period vectors in a
565 periodic system under constant external stress," *Can. J. Phys.*, **93**
574 <div id="ref-Tuckerman2006">
576 .. _refTuckerman2006:
578 :sup:`41` M.E. Tuckerman, J. Alejandre, R. López-Rendón, A.L. Jochim,
579 and G.J. Martyna, "A Liouville-operator derived measure-preserving
580 integrator for molecular dynamics simulations in the isothermal-isobaric
581 ensemble," *J. Phys. A.*, **59** 5629–5651 (2006).
589 <div id="ref-Yu2010">
593 :sup:`42` T.-Q. Yu, J. Alejandre, R. Lopez-Rendon, G.J. Martyna, and
594 M.E. Tuckerman, "Measure-preserving integrators for molecular dynamics
595 in the isothermal-isobaric ensemble derived from the liouville
596 operator," *Chem. Phys.*, **370** 294–305 (2010).
604 <div id="ref-Dick58">
608 :sup:`43` B.G. Dick and A.W. Overhauser, "Theory of the dielectric
609 constants of alkali halide crystals," *Phys. Rev.*, **112** 90–103
618 <div id="ref-Jordan95">
622 :sup:`44` P.C. Jordan, P.J. van Maaren, J. Mavri, D. van der Spoel, and
623 H.J.C. Berendsen, "Towards phase transferable potential functions:
624 Methodology and application to nitrogen," *J. Chem. Phys.*, **103**
633 <div id="ref-Maaren2001a">
637 :sup:`45` P.J. van Maaren and D. van der Spoel, "Molecular dynamics
638 simulations of a water with a novel shell-model potential," *J. Phys.
639 Chem. B.*, **105** 2618–2626 (2001).
647 <div id="ref-Ryckaert77">
651 :sup:`46` J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen, "Numerical
652 integration of the cartesian equations of motion of a system with
653 constraints; molecular dynamics of n-alkanes," *J. Comp. Phys.*, **23**
662 <div id="ref-Miyamoto92">
666 :sup:`47` S. Miyamoto and P.A. Kollman, "SETTLE: An analytical version
667 of the SHAKE and RATTLE algorithms for rigid water models," *J. Comp.
668 Chem.*, **13** 952–962 (1992).
676 <div id="ref-Andersen1983a">
678 .. _refAndersen1983a:
680 :sup:`48` H.C. Andersen, "RATTLE: A ‘Velocity’ version of the SHAKE
681 algorithm for molecular dynamics calculations," *J. Comp. Phys.*, **52**
690 <div id="ref-Hess97">
694 :sup:`49` B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije,
695 "LINCS: A linear constraint solver for molecular simulations," *J. Comp.
696 Chem.*, **18** 1463–1472 (1997).
704 <div id="ref-Hess2008a">
708 :sup:`50` B. Hess, "P-LINCS: A parallel linear constraint solver for
709 molecular simulation," *J. Chem. Theory Comput.*, **4** 116–122 (2007).
717 <div id="ref-Goga2012">
721 :sup:`51` N. Goga, A.J. Rzepiela, A.H. de Vries, S.J. Marrink, and
722 H.J.C. Berendsen, "Efficient algorithms for Langevin and DPD dynamics,"
723 *J. Chem. Theory Comput.*, **8** 3637–3649 (2012).
731 <div id="ref-Byrd95a">
735 :sup:`52` R.H. Byrd, P. Lu, and J. Nocedal, "A limited memory algorithm
736 for bound constrained optimization," *SIAM J. Scientif. Statistic.
737 Comput.*, **16** 1190–1208 (1995).
745 <div id="ref-Zhu97a">
749 :sup:`53` C. Zhu, R.H. Byrd, and J. Nocedal, "L-BFGS-B: Algorithm 778:
750 L-BFGS-B, FORTRAN routines for large scale bound constrained
751 optimization," *ACM Trans. Math. Softw.*, **23** 550–560 (1997).
759 <div id="ref-Levitt83">
763 :sup:`54` M. Levitt, C. Sander, and P.S. Stern, "The normal modes of a
764 protein: Native bovine pancreatic trypsin inhibitor," *Int. J. Quant.
765 Chem: Quant. Biol. Symp.*, **10** 181–199 (1983).
777 :sup:`55` N. G\ :math:`\bar{\rm o}`, T. Noguti, and T. Nishikawa,
778 "Dynamics of a small globular protein in terms of low-frequency
779 vibrational modes," *Proc. Natl. Acad. Sci. USA*, **80** 3696–3700
788 <div id="ref-BBrooks83b">
792 :sup:`56` B. Brooks and M. Karplus, "Harmonic dynamics of proteins:
793 Normal modes and fluctuations in bovine pancreatic trypsin inhibitor,"
794 *Proc. Natl. Acad. Sci. USA*, **80** 6571–6575 (1983).
802 <div id="ref-Hayward95b">
806 :sup:`57` S. Hayward and N. G\ :math:`\bar{\rm o}`, "Collective variable
807 description of native protein dynamics," *Annu. Rev. Phys. Chem.*,
808 **46** 223–250 (1995).
816 <div id="ref-Bennett1976">
820 :sup:`58` C.H. Bennett, "Efficient Estimation of Free Energy Differences
821 from Monte Carlo Data," *J. Comp. Phys.*, **22** 245–268 (1976).
829 <div id="ref-Shirts2008">
833 :sup:`59` M.R. Shirts and J.D. Chodera, "Statistically optimal analysis
834 of multiple equilibrium simulations," *J. Chem. Phys.*, **129** 124105
843 <div id="ref-Hukushima96a">
847 :sup:`60` K. Hukushima and K. Nemoto, "Exchange Monte Carlo Method and
848 Application to Spin Glass Simulations," *J. Phys. Soc. Jpn.*, **65**
857 <div id="ref-Sugita99">
861 :sup:`61` Y. Sugita and Y. Okamoto, "Replica-exchange molecular dynamics
862 method for protein folding," *Chem. Phys. Lett.*, **314** 141–151
871 <div id="ref-Seibert2005a">
875 :sup:`62` M. Seibert, A. Patriksson, B. Hess, and D. van der Spoel,
876 "Reproducible polypeptide folding and structure prediction using
877 molecular dynamics simulations," *J. Mol. Biol.*, **354** 173–183
886 <div id="ref-Okabe2001a">
890 :sup:`63` T. Okabe, M. Kawata, Y. Okamoto, and M. Mikami,
891 "Replica-exchange Monte Carlo method for the isobaric-isothermal
892 ensemble," *Chem. Phys. Lett.*, **335** 435–439 (2001).
900 <div id="ref-Chodera2011">
904 :sup:`64` J.D. Chodera and M.R. Shirts, "Replica exchange and expanded
905 ensemble simulations as gibbs sampling: Simple improvements for enhanced
906 mixing," *J. Chem. Phys.*, **135** 194110 (2011).
914 <div id="ref-Degroot96a">
918 :sup:`65` B.L. de Groot, A. Amadei, D.M.F. van Aalten, and H.J.C.
919 Berendsen, "Towards an exhaustive sampling of the configurational spaces
920 of the two forms of the peptide hormone guanylin," *J. Biomol. Str.
921 Dyn.*, **13** [5] 741–751 (1996).
929 <div id="ref-Degroot96b">
933 :sup:`66` B.L. de Groot, A. Amadei, R.M. Scheek, N.A.J. van Nuland, and
934 H.J.C. Berendsen, "An extended sampling of the configurational space of
935 HPr from *E. coli*," *PROTEINS: Struct. Funct. Gen.*, **26** 314–322
944 <div id="ref-Lange2006a">
948 :sup:`67` O.E. Lange, L.V. Schafer, and H. Grubmuller, "Flooding in
949 GROMACS: Accelerated barrier crossings in molecular dynamics," *J. Comp.
950 Chem.*, **27** 1693–1702 (2006).
958 <div id="ref-Lyubartsev1992">
960 .. _refLyubartsev1992:
962 :sup:`68` A.P. Lyubartsev, A.A. Martsinovski, S.V. Shevkunov, and P.N.
963 Vorontsov-Velyaminov, "New approach to Monte Carlo calculation of the
964 free energy: Method of expanded ensembles," *J. Chem. Phys.*, **96**
973 <div id="ref-Liem1991">
977 :sup:`69` S.Y. Liem, D. Brown, and J.H.R. Clarke, "Molecular dynamics
978 simulations on distributed memory machines," *Comput. Phys. Commun.*,
979 **67** [2] 261–267 (1991).
987 <div id="ref-Shaw2006">
991 :sup:`70` K.J. Bowers, R.O. Dror, and D.E. Shaw, "The midpoint method
992 for parallelization of particle simulations," *J. Chem. Phys.*, **124**
993 [18] 184109–184109 (2006).
1001 <div id="ref-Spoel2006a">
1005 :sup:`72` D. van der Spoel and P.J. van Maaren, "The origin of layer
1006 structure artifacts in simulations of liquid water," *J. Chem. Theory
1007 Comput.*, **2** 1–11 (2006).
1015 <div id="ref-Ohmine1988">
1019 :sup:`73` I. Ohmine, H. Tanaka, and P.G. Wolynes, "Large local energy
1020 fluctuations in water. II. Cooperative motions and fluctuations," *J.
1021 Chem. Phys.*, **89** 5852–5860 (1988).
1029 <div id="ref-Kitchen1990">
1033 :sup:`74` D.B. Kitchen, F. Hirata, J.D. Westbrook, R. Levy, D. Kofke,
1034 and M. Yarmush, "Conserving energy during molecular dynamics simulations
1035 of water, proteins, and proteins in water," *J. Comp. Chem.*, **11**
1044 <div id="ref-Guenot1993">
1048 :sup:`75` J. Guenot and P.A. Kollman, "Conformational and energetic
1049 effects of truncating nonbonded interactions in an aqueous protein
1050 dynamics simulation," *J. Comp. Chem.*, **14** 295–311 (1993).
1058 <div id="ref-Steinbach1994">
1060 .. _refSteinbach1994:
1062 :sup:`76` P.J. Steinbach and B.R. Brooks, "New spherical-cutoff methods
1063 for long-range forces in macromolecular simulation," *J. Comp. Chem.*,
1064 **15** 667–683 (1994).
1072 <div id="ref-gromos96">
1076 :sup:`77` W.F. van Gunsteren, S.R. Billeter, A.A. Eising, P.H.
1077 Hünenberger, P. Krüger, A.E. Mark, W.R.P. Scott, and I.G. Tironi,
1078 *Biomolecular simulation: The GROMOS96 manual and user guide*.
1079 Hochschulverlag AG an der ETH Zürich, Zürich, Switzerland, 1996.
1087 <div id="ref-biomos">
1091 :sup:`78` W.F. van Gunsteren and H.J.C. Berendsen, *Gromos-87 manual*.
1092 Biomos BV, Nijenborgh 4, 9747 AG Groningen, The Netherlands, 1987.
1100 <div id="ref-Morse29">
1104 :sup:`79` P.M. Morse, "Diatomic molecules according to the wave
1105 mechanics. II. vibrational levels." *Phys. Rev.*, **34** 57–64 (1929).
1113 <div id="ref-Berendsen81">
1117 :sup:`80` H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J.
1118 Hermans, "Interaction models for water in relation to protein
1119 hydration"; pp. 331–342 in *Intermolecular forces*. Edited by B.
1120 Pullman. D. Reidel Publishing Company, Dordrecht, 1981.
1128 <div id="ref-Ferguson95">
1132 :sup:`81` D.M. Ferguson, "Parametrization and evaluation of a flexible
1133 water model," *J. Comp. Chem.*, **16** 501–511 (1995).
1141 <div id="ref-Warner72">
1145 :sup:`82` H.R. Warner Jr., "Kinetic theory and rheology of dilute
1146 suspensions of finitely extendible dumbbells," *Ind. Eng. Chem.
1147 Fundam.*, **11** [3] 379–387 (1972).
1155 <div id="ref-MonicaGoga2013">
1157 .. _refMonicaGoga2013:
1159 :sup:`83` M. Bulacu, N. Goga, W. Zhao, G. Rossi, L. Monticelli, X.
1160 Periole, D. Tieleman, and S. Marrink, "Improved angle potentials for
1161 coarse-grained molecular dynamics simulations," *J. Chem. Phys.*,
1162 **123** [11] (2005).
1170 <div id="ref-BBrooks83">
1174 :sup:`84` B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S.
1175 Swaminathan, and M. Karplus, "CHARMM: A program for macromolecular
1176 energy, minimization, and dynamics calculation," *J. Comp. Chem.*, **4**
1185 <div id="ref-Lawrence2003b">
1187 .. _refLawrence2003b:
1189 :sup:`85` C.P. Lawrence and J.L. Skinner, "Flexible TIP4P model for
1190 molecular dynamics simulation of liquid water," *Chem. Phys. Lett.*,
1191 **372** 842–847 (2003).
1199 <div id="ref-Jorgensen1996">
1201 .. _refJorgensen1996:
1203 :sup:`86` W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives,
1204 "Development and testing of the oPLS all-atom force field on
1205 conformational energetics and properties of organic liquids," *J. Am.
1206 Chem. Soc.*, **118** 11225–11236 (1996).
1214 <div id="ref-Robertson2015a">
1216 .. _refRobertson2015a:
1218 :sup:`87` M.J. Robertson, J. Tirado-Rives, and W.L. Jorgensen, "Improved
1219 peptide and protein torsional energetics with the oPLS-aA force field,"
1220 *J. Chem. Theory Comput.*, **11** 3499–3509 (2015).
1228 <div id="ref-BulacuGiessen2005">
1230 .. _refBulacuGiessen2005:
1232 :sup:`88` M. Bulacu and E. van der Giessen, "Effect of bending and
1233 torsion rigidity on self-diffusion in polymer melts: A
1234 molecular-dynamics study," *JCTC*, **9** [8] 3282–3292 (2013).
1242 <div id="ref-ScottScheragator1966">
1244 .. _refScottScheragator1966:
1246 :sup:`89` R.A. Scott and H. Scheraga, "Conformational analysis of
1247 macromolecules," *J. Chem. Phys.*, **44** 3054–3069 (1966).
1255 <div id="ref-PaulingBond">
1259 :sup:`90` L. Pauling, *The nature of chemical bond*. Cornell University
1260 Press, Ithaca; New York, 1960.
1268 <div id="ref-Torda89">
1272 :sup:`91` A.E. Torda, R.M. Scheek, and W.F. van Gunsteren,
1273 "Time-dependent distance restraints in molecular dynamics simulations,"
1274 *Chem. Phys. Lett.*, **157** 289–294 (1989).
1282 <div id="ref-Hess2003">
1286 :sup:`92` B. Hess and R.M. Scheek, "Orientation restraints in molecular
1287 dynamics simulations using time and ensemble averaging," *J. Magn.
1288 Reson.*, **164** 19–27 (2003).
1296 <div id="ref-Lopes2013a">
1300 :sup:`93` P.E.M. Lopes, J. Huang, J. Shim, Y. Luo, H. Li, B. Roux, and
1301 J. MacKerell Alexander D., "Polarizable force field for peptides and
1302 proteins based on the classical drude oscillator," *J. Chem. Theory
1303 Comput*, **9** 5430–5449 (2013).
1311 <div id="ref-HYu2010">
1315 :sup:`94` H. Yu, T.W. Whitfield, E. Harder, G. Lamoureux, I. Vorobyov,
1316 V.M. Anisimov, A.D. MacKerell, Jr., and B. Roux, "Simulating Monovalent
1317 and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force
1318 Field," *J. Chem. Theory Comput.*, **6** 774–786 (2010).
1326 <div id="ref-Thole81">
1330 :sup:`95` B.T. Thole, "Molecular polarizabilities with a modified dipole
1331 interaction," *Chem. Phys.*, **59** 341–345 (1981).
1339 <div id="ref-Lamoureux2003a">
1341 .. _refLamoureux2003a:
1343 :sup:`96` G. Lamoureux and B. Roux, "Modeling induced polarization with
1344 classical drude oscillators: Theory and molecular dynamics simulation
1345 algorithm," *J. Chem. Phys.*, **119** 3025–3039 (2003).
1353 <div id="ref-Lamoureux2003b">
1355 .. _refLamoureux2003b:
1357 :sup:`97` G. Lamoureux, A.D. MacKerell, and B. Roux, "A simple
1358 polarizable model of water based on classical drude oscillators," *J.
1359 Chem. Phys.*, **119** 5185–5197 (2003).
1367 <div id="ref-Noskov2005a">
1371 :sup:`98` S.Y. Noskov, G. Lamoureux, and B. Roux, "Molecular dynamics
1372 study of hydration in ethanol-water mixtures using a polarizable force
1373 field," *J. Phys. Chem. B.*, **109** 6705–6713 (2005).
1381 <div id="ref-Gunsteren98a">
1383 .. _refGunsteren98a:
1385 :sup:`99` W.F. van Gunsteren and A.E. Mark, "Validation of molecular
1386 dynamics simulations," *J. Chem. Phys.*, **108** 6109–6116 (1998).
1394 <div id="ref-Beutler94">
1398 :sup:`100` T.C. Beutler, A.E. Mark, R.C. van Schaik, P.R. Greber, and
1399 W.F. van Gunsteren, "Avoiding singularities and numerical instabilities
1400 in free energy calculations based on molecular simulations," *Chem.
1401 Phys. Lett.*, **222** 529–539 (1994).
1409 <div id="ref-Pham2011">
1413 :sup:`101` T.T. Pham and M.R. Shirts, "Identifying low variance pathways
1414 for free energy calculations of molecular transformations in solution
1415 phase," *J. Chem. Phys.*, **135** 034114 (2011).
1423 <div id="ref-Pham2012">
1427 :sup:`102` T.T. Pham and M.R. Shirts, "Optimal pairwise and non-pairwise
1428 alchemical pathways for free energy calculations of molecular
1429 transformation in solution phase," *J. Chem. Phys.*, **136** 124120
1438 <div id="ref-Jorgensen88">
1442 :sup:`103` W.L. Jorgensen and J. Tirado-Rives, "The OPLS potential
1443 functions for proteins. energy minimizations for crystals of cyclic
1444 peptides and crambin," *J. Am. Chem. Soc.*, **110** 1657–1666 (1988).
1452 <div id="ref-Berendsen84b">
1454 .. _refBerendsen84b:
1456 :sup:`104` H.J.C. Berendsen and W.F. van Gunsteren, "Molecular dynamics
1457 simulations: Techniques and approaches"; pp. 475–500 in *Molecular
1458 liquids-dynamics and interactions*. Edited by A.J.B. et al. Reidel,
1459 Dordrecht, The Netherlands, 1984.
1467 <div id="ref-Ewald21">
1471 :sup:`105` P.P. Ewald, "Die Berechnung optischer und elektrostatischer
1472 Gitterpotentiale," *Ann. Phys.*, **64** 253–287 (1921).
1480 <div id="ref-Hockney81">
1484 :sup:`106` R.W. Hockney and J.W. Eastwood, *Computer simulation using
1485 particles*. McGraw-Hill, New York, 1981.
1493 <div id="ref-Ballenegger2012">
1495 .. _refBallenegger2012:
1497 :sup:`107` V. Ballenegger, J.J. Cerdà, and C. Holm, "How to convert SPME
1498 to P3M: Influence functions and error estimates," *J. Chem. Theory
1499 Comput.*, **8** [3] 936–947 (2012).
1507 <div id="ref-Allen87">
1511 :sup:`108` M.P. Allen and D.J. Tildesley, *Computer simulations of
1512 liquids*. Oxford Science Publications, Oxford, 1987.
1520 <div id="ref-Wennberg13">
1524 :sup:`109` C.L. Wennberg, T. Murtola, B. Hess, and E. Lindahl,
1525 "Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical
1526 Effects on Surface Tension and Lipid Properties," *J. Chem. Theory
1527 Comput.*, **9** 3527–3537 (2013).
1535 <div id="ref-Oostenbrink2004">
1537 .. _refOostenbrink2004:
1539 :sup:`110` C. Oostenbrink, A. Villa, A.E. Mark, and W.F. Van Gunsteren,
1540 "A biomolecular force field based on the free enthalpy of hydration and
1541 solvation: The GROMOS force-field parameter sets 53A5 and 53A6,"
1542 *Journal of Computational Chemistry*, **25** [13] 1656–1676 (2004).
1550 <div id="ref-Cornell1995">
1554 :sup:`111` W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.R. Merz
1555 Jr., D.M. Ferguson, D.C. Spellmeyer, and T. Fox *et al.*, "A Second
1556 Generation Force Field for the Simulation of Proteins, Nucleic Acids,
1557 and Organic Molecules," *J. Am. Chem. Soc.*, **117** [19] 5179–5197
1566 <div id="ref-Kollman1996">
1570 :sup:`112` P.A. Kollman, "Advances and Continuing Challenges in
1571 Achieving Realistic and Predictive Simulations of the Properties of
1572 Organic and Biological Molecules," *Acc. Chem. Res.*, **29** [10]
1581 <div id="ref-Wang2000">
1585 :sup:`113` J. Wang, P. Cieplak, and P.A. Kollman, "How Well Does a
1586 Restrained Electrostatic Potential (RESP) Model Perform in Calculating
1587 Conformational Energies of Organic and Biological Molecules?" *J. Comp.
1588 Chem.*, **21** [12] 1049–1074 (2000).
1596 <div id="ref-Hornak2006">
1600 :sup:`114` V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and
1601 C. Simmerling, "Comparison of Multiple Amber Force Fields and
1602 Development of Improved Protein Backbone Parameters," *PROTEINS: Struct.
1603 Funct. Gen.*, **65** 712–725 (2006).
1611 <div id="ref-Lindorff2010">
1613 .. _refLindorff2010:
1615 :sup:`115` K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J.L.
1616 Klepeis, R.O. Dorr, and D.E. Shaw, "Improved side-chain torsion
1617 potentials for the AMBER ff99SB protein force field," *PROTEINS: Struct.
1618 Funct. Gen.*, **78** 1950–1958 (2010).
1626 <div id="ref-Duan2003">
1630 :sup:`116` Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, G. Xiong, W. Zhang,
1631 R. Yang, and P. Cieplak *et al.*, "A Point-Charge Force Field for
1632 Molecular Mechanics Simulations of Proteins Based on Condensed-Phase
1633 Quantum Mechanical Calculations," *J. Comp. Chem.*, **24** [16]
1642 <div id="ref-Garcia2002">
1646 :sup:`117` A.E. García and K.Y. Sanbonmatsu, "\ :math:`\alpha`-Helical
1647 stabilization by side chain shielding of backbone hydrogen bonds,"
1648 *Proc. Natl. Acad. Sci. USA*, **99** [5] 2782–2787 (2002).
1656 <div id="ref-mackerell04">
1660 :sup:`118` J. MacKerell A. D., M. Feig, and C.L. Brooks III, "Extending
1661 the treatment of backbone energetics in protein force fields:
1662 Limitations of gas-phase quantum mechanics in reproducing protein
1663 conformational distributions in molecular dynamics simulations," *J.
1664 Comp. Chem.*, **25** [11] 1400–15 (2004).
1672 <div id="ref-mackerell98">
1676 :sup:`119` A.D. MacKerell, D. Bashford, Bellott, R.L. Dunbrack, J.D.
1677 Evanseck, M.J. Field, S. Fischer, and J. Gao *et al.*, "All-atom
1678 empirical potential for molecular modeling and dynamics studies of
1679 proteins," *J. Phys. Chem. B.*, **102** [18] 3586–3616 (1998).
1687 <div id="ref-feller00">
1691 :sup:`120` S.E. Feller and A.D. MacKerell, "An improved empirical
1692 potential energy function for molecular simulations of phospholipids,"
1693 *J. Phys. Chem. B.*, **104** [31] 7510–7515 (2000).
1701 <div id="ref-foloppe00">
1705 :sup:`121` N. Foloppe and A.D. MacKerell, "All-atom empirical force
1706 field for nucleic acids: I. Parameter optimization based on small
1707 molecule and condensed phase macromolecular target data," *J. Comp.
1708 Chem.*, **21** [2] 86–104 (2000).
1716 <div id="ref-Mac2000">
1720 :sup:`122` A.D. MacKerell and N.K. Banavali, "All-atom empirical force
1721 field for nucleic acids: II. application to molecular dynamics
1722 simulations of DNA and RNA in solution," *J. Comp. Chem.*, **21** [2]
1731 <div id="ref-Larsson10">
1735 :sup:`123` P. Larsson and E. Lindahl, "A High-Performance
1736 Parallel-Generalized Born Implementation Enabled by Tabulated
1737 Interaction Rescaling," *J. Comp. Chem.*, **31** [14] 2593–2600 (2010).
1745 <div id="ref-Bjelkmar10">
1749 :sup:`124` P. Bjelkmar, P. Larsson, M.A. Cuendet, B. Hess, and E.
1750 Lindahl, "Implementation of the CHARMM force field in GROMACS: Analysis
1751 of protein stability effects from correction maps, virtual interaction
1752 sites, and water models," *J. Chem. Theory Comput.*, **6** 459–466
1761 <div id="ref-kohlmeyer2016">
1763 .. _refkohlmeyer2016:
1765 :sup:`125` A. Kohlmeyer and J. Vermaas, *TopoTools: Release 1.6 with
1766 CHARMM export in topogromacs*, (2016).
1774 <div id="ref-bereau12">
1778 :sup:`126` T. Bereau, Z.-J. Wang, and M. Deserno, *Solvent-free
1779 coarse-grained model for unbiased high-resolution protein-lipid
1780 interactions*, (n.d.).
1788 <div id="ref-wang_jpcb10">
1792 :sup:`127` Z.-J. Wang and M. Deserno, "A systematically coarse-grained
1793 solvent-free model for quantitative phospholipid bilayer simulations,"
1794 *J. Phys. Chem. B.*, **114** [34] 11207–11220 (2010).
1802 <div id="ref-Jorgensen83">
1806 :sup:`128` W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey,
1807 and M.L. Klein, "Comparison of simple potential functions for simulating
1808 liquid water," *J. Chem. Phys.*, **79** 926–935 (1983).
1816 <div id="ref-iupac70">
1820 :sup:`129` IUPAC-IUB Commission on Biochemical Nomenclature,
1821 "Abbreviations and Symbols for the Description of the Conformation of
1822 Polypeptide Chains. Tentative Rules (1969)," *Biochemistry*, **9**
1831 <div id="ref-Mahoney2000a">
1833 .. _refMahoney2000a:
1835 :sup:`130` M.W. Mahoney and W.L. Jorgensen, "A five-site model for
1836 liquid water and the reproduction of the density anomaly by rigid,
1837 nonpolarizable potential functions," *J. Chem. Phys.*, **112** 8910–8922
1846 <div id="ref-Ryckaert78">
1850 :sup:`131` J.P. Ryckaert and A. Bellemans, "Molecular dynamics of liquid
1851 alkanes," *Far. Disc. Chem. Soc.*, **66** 95–106 (1978).
1859 <div id="ref-Loof92">
1863 :sup:`132` H. de Loof, L. Nilsson, and R. Rigler, "Molecular dynamics
1864 simulations of galanin in aqueous and nonaqueous solution," *J. Am.
1865 Chem. Soc.*, **114** 4028–4035 (1992).
1873 <div id="ref-Buuren93a">
1877 :sup:`133` A.R. van Buuren and H.J.C. Berendsen, "Molecular Dynamics
1878 simulation of the stability of a 22 residue alpha-helix in water and 30%
1879 trifluoroethanol," *Biopolymers*, **33** 1159–1166 (1993).
1887 <div id="ref-RMNeumann1980a">
1889 .. _refRMNeumann1980a:
1891 :sup:`134` R.M. Neumann, "Entropic approach to Brownian Movement," *Am.
1892 J. Phys.*, **48** 354–357 (1980).
1900 <div id="ref-Jarzynski1997a">
1902 .. _refJarzynski1997a:
1904 :sup:`135` C. Jarzynski, "Nonequilibrium equality for free energy
1905 differences," *Phys. Rev. Lett.*, **78** [14] 2690–2693 ().
1913 <div id="ref-Engin2010a">
1917 :sup:`136` M.S. O. Engin A. Villa and B. Hess, "Driving forces for
1918 adsorption of amphiphilic peptides to air-water interface," *J. Phys.
1927 <div id="ref-lindahl2014accelerated">
1929 .. _reflindahl2014accelerated:
1931 :sup:`137` V. Lindahl, J. Lidmar, and B. Hess, "Accelerated weight
1932 histogram method for exploring free energy landscapes," *The Journal of
1933 chemical physics*, **141** [4] 044110 (2014).
1941 <div id="ref-wang2001efficient">
1943 .. _refwang2001efficient:
1945 :sup:`138` F. Wang and D. Landau, "Efficient, multiple-range random walk
1946 algorithm to calculate the density of states," *Physical review
1947 letters*, **86** [10] 2050 (2001).
1955 <div id="ref-huber1994local">
1957 .. _refhuber1994local:
1959 :sup:`139` T. Huber, A.E. Torda, and W.F. van Gunsteren, "Local
1960 elevation: A method for improving the searching properties of molecular
1961 dynamics simulation," *Journal of computer-aided molecular design*,
1962 **8** [6] 695–708 (1994).
1970 <div id="ref-laio2002escaping">
1972 .. _reflaio2002escaping:
1974 :sup:`140` A. Laio and M. Parrinello, "Escaping free-energy minima,"
1975 *Proceedings of the National Academy of Sciences*, **99** [20]
1984 <div id="ref-belardinelli2007fast">
1986 .. _refbelardinelli2007fast:
1988 :sup:`141` R. Belardinelli and V. Pereyra, "Fast algorithm to calculate
1989 density of states," *Physical Review E*, **75** [4] 046701 (2007).
1997 <div id="ref-barducci2008well">
1999 .. _refbarducci2008well:
2001 :sup:`142` A. Barducci, G. Bussi, and M. Parrinello, "Well-tempered
2002 metadynamics: A smoothly converging and tunable free-energy method,"
2003 *Physical review letters*, **100** [2] 020603 (2008).
2011 <div id="ref-lindahl2017sequence">
2013 .. _reflindahl2017sequence:
2015 :sup:`143` V. Lindahl, A. Villa, and B. Hess, "Sequence dependency of
2016 canonical base pair opening in the dNA double helix," *PLoS
2017 computational biology*, **13** [4] e1005463 (2017).
2025 <div id="ref-sivak2012thermodynamic">
2027 .. _refsivak2012thermodynamic:
2029 :sup:`144` D.A. Sivak and G.E. Crooks, "Thermodynamic metrics and
2030 optimal paths," *Physical review letters*, **108** [19] 190602 (2012).
2038 <div id="ref-Kutzner2011">
2042 :sup:`145` C. Kutzner, J. Czub, and H. Grubmüller, "Keep it flexible:
2043 Driving macromolecular rotary motions in atomistic simulations with
2044 GROMACS," *J. Chem. Theory Comput.*, **7** 1381–1393 (2011).
2052 <div id="ref-Caleman2008a">
2054 .. _refCaleman2008a:
2056 :sup:`146` C. Caleman and D. van der Spoel, "Picosecond Melting of Ice
2057 by an Infrared Laser Pulse - A simulation study," *Angew. Chem., Int.
2058 Ed. Engl.*, **47** 1417–1420 (2008).
2066 <div id="ref-Kutzner2011b">
2068 .. _refKutzner2011b:
2070 :sup:`147` C. Kutzner, H. Grubmüller, B.L. de Groot, and U. Zachariae,
2071 "Computational electrophysiology: The molecular dynamics of ion channel
2072 permeation and selectivity in atomistic detail," *Biophys. J.*, **101**
2081 <div id="ref-feenstra99">
2085 :sup:`148` K.A. Feenstra, B. Hess, and H.J.C. Berendsen, "Improving
2086 efficiency of large time-scale molecular dynamics simulations of
2087 hydrogen-rich systems," *J. Comp. Chem.*, **20** 786–798 (1999).
2095 <div id="ref-Hess2002a">
2099 :sup:`149` B. Hess, "Determining the shear viscosity of model liquids
2100 from molecular dynamics," *J. Chem. Phys.*, **116** 209–217 (2002).
2108 <div id="ref-mopac">
2112 :sup:`150` M.J.S. Dewar, "Development and status of MINDO/3 and MNDO,"
2113 *J. Mol. Struct.*, **100** 41 (1983).
2121 <div id="ref-gamess-uk">
2125 :sup:`151` M.F. Guest, R.J. Harrison, J.H. van Lenthe, and L.C.H. van
2126 Corler, "Computational chemistry on the FPS-X64 scientific computers -
2127 Experience on single- and multi-processor systems," *Theor. Chim. Act.*,
2140 :sup:`152` M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A.
2141 Robb, J.R. Cheeseman, J.A. Montgomery Jr., and T. Vreven *et al.*,
2142 *Gaussian 03, Revision C.02*, (n.d.).
2150 <div id="ref-Car85a">
2154 :sup:`153` R. Car and M. Parrinello, "Unified approach for molecular
2155 dynamics and density-functional theory," *Phys. Rev. Lett.*, **55**
2164 <div id="ref-Field90a">
2168 :sup:`154` M. Field, P.A. Bash, and M. Karplus, "A combined quantum
2169 mechanical and molecular mechanical potential for molecular dynamics
2170 simulation," *J. Comp. Chem.*, **11** 700 (1990).
2178 <div id="ref-Maseras96a">
2182 :sup:`155` F. Maseras and K. Morokuma, "IMOMM: A New Ab Initio +
2183 Molecular Mechanics Geometry Optimization Scheme of Equilibrium
2184 Structures and Transition States," *J. Comp. Chem.*, **16** 1170–1179
2193 <div id="ref-Svensson96a">
2197 :sup:`156` M. Svensson, S. Humbel, R.D.J. Froes, T. Matsubara, S.
2198 Sieber, and K. Morokuma, "ONIOM a multilayered integrated MO + MM method
2199 for geometry optimizations and single point energy predictions. a test
2200 for Diels-Alder reactions and Pt(P(t-Bu)3)2 + H2 oxidative addition,"
2201 *J. Phys. Chem.*, **100** 19357 (1996).
2209 <div id="ref-Yesylevskyy2007">
2211 .. _refYesylevskyy2007:
2213 :sup:`157` S. Yesylevskyy, "ProtSqueeze: Simple and effective automated
2214 tool for setting up membrane protein simulations," *J. Chem. Inf.
2215 Model.*, **47** 1986–1994 (2007).
2223 <div id="ref-Wolf2010">
2227 :sup:`158` M. Wolf, M. Hoefling, C. Aponte-Santamaría, H. Grubmüller,
2228 and G. Groenhof, "g\_membed: Efficient insertion of a membrane protein
2229 into an equilibrated lipid bilayer with minimal perturbation," *J. Comp.
2230 Chem.*, **31** 2169–2174 (2010).
2238 <div id="ref-Spoel97a">
2242 :sup:`159` D. van der Spoel and H.J.C. Berendsen, "Molecular dynamics
2243 simulations of Leu-enkephalin in water and DMSO," *Biophys. J.*, **72**
2252 <div id="ref-PSmith93c">
2256 :sup:`160` P.E. Smith and W.F. van Gunsteren, "The Viscosity of SPC and
2257 SPC/E Water," *Chem. Phys. Lett.*, **215** 315–318 (1993).
2265 <div id="ref-Balasubramanian96">
2267 .. _refBalasubramanian96:
2269 :sup:`161` S. Balasubramanian, C.J. Mundy, and M.L. Klein, "Shear
2270 viscosity of polar fluids: Molecular dynamics calculations of water,"
2271 *J. Chem. Phys.*, **105** 11190–11195 (1996).
2279 <div id="ref-lmfit">
2283 :sup:`162` J. Wuttke, *Lmfit*, (2013).
2291 <div id="ref-Steen-Saethre2014a">
2293 .. _refSteen-Saethre2014a:
2295 :sup:`163` B. Steen-Sæthre, A.C. Hoffmann, and D. van der Spoel, "Order
2296 parameters and algorithmic approaches for detection and demarcation of
2297 interfaces in hydrate-fluid and ice-fluid systems," *J. Chem. Theor.
2298 Comput.*, **10** 5606–5615 (2014).
2306 <div id="ref-Palmer1994a">
2310 :sup:`164` B.J. Palmer, "Transverse-current autocorrelation-function
2311 calculations of the shear viscosity for molecular liquids." *Phys. Rev.
2312 E*, **49** 359–366 (1994).
2320 <div id="ref-Wensink2003a">
2322 .. _refWensink2003a:
2324 :sup:`165` E.J.W. Wensink, A.C. Hoffmann, P.J. van Maaren, and D. van
2325 der Spoel, "Dynamic properties of water/alcohol mixtures studied by
2326 computer simulation," *J. Chem. Phys.*, **119** 7308–7317 (2003).
2334 <div id="ref-Guo2002b">
2338 :sup:`166` G.-J. Guo, Y.-G. Zhang, K. Refson, and Y.-J. Zhao, "Viscosity
2339 and stress autocorrelation function in supercooled water: A molecular
2340 dynamics study," *Mol. Phys.*, **100** 2617–2627 (2002).
2348 <div id="ref-Fanourgakis2012a">
2350 .. _refFanourgakis2012a:
2352 :sup:`167` G.S. Fanourgakis, J.S. Medina, and R. Prosmiti, "Determining
2353 the bulk viscosity of rigid water models," *J. Phys. Chem. A*, **116**
2362 <div id="ref-Spoel96b">
2366 :sup:`168` D. van der Spoel, H.J. Vogel, and H.J.C. Berendsen,
2367 "Molecular dynamics simulations of N-terminal peptides from a nucleotide
2368 binding protein," *PROTEINS: Struct. Funct. Gen.*, **24** 450–466
2377 <div id="ref-Amadei93">
2381 :sup:`169` A. Amadei, A.B.M. Linssen, and H.J.C. Berendsen, "Essential
2382 dynamics of proteins," *PROTEINS: Struct. Funct. Gen.*, **17** 412–425
2391 <div id="ref-Hess2002b">
2395 :sup:`170` B. Hess, "Convergence of sampling in protein simulations,"
2396 *Phys. Rev. **E***, **65** 031910 (2002).
2404 <div id="ref-Hess2000">
2408 :sup:`171` B. Hess, "Similarities between principal components of
2409 protein dynamics and random diffusion," *Phys. Rev. **E***, **62**
2418 <div id="ref-Mu2005a">
2422 :sup:`172` Y. Mu, P.H. Nguyen, and G. Stock, "Energy landscape of a
2423 small peptide revelaed by dihedral angle principal component analysis,"
2424 *PROTEINS: Struct. Funct. Gen.*, **58** 45–52 (2005).
2432 <div id="ref-Spoel2006b">
2436 :sup:`173` D. van der Spoel, P.J. van Maaren, P. Larsson, and N.
2437 Timneanu, "Thermodynamics of hydrogen bonding in hydrophilic and
2438 hydrophobic media," *J. Phys. Chem. B.*, **110** 4393–4398 (2006).
2446 <div id="ref-Luzar96b">
2450 :sup:`174` A. Luzar and D. Chandler, "Hydrogen-bond kinetics in liquid
2451 water," *Nature*, **379** 55–57 (1996).
2459 <div id="ref-Luzar2000a">
2463 :sup:`175` A. Luzar, "Resolving the hydrogen bond dynamics conundrum,"
2464 *J. Chem. Phys.*, **113** 10663–10675 (2000).
2472 <div id="ref-Kabsch83">
2476 :sup:`176` W. Kabsch and C. Sander, "Dictionary of protein secondary
2477 structure: Pattern recognition of hydrogen-bonded and geometrical
2478 features," *Biopolymers*, **22** 2577–2637 (1983).
2486 <div id="ref-Bekker93b">
2490 :sup:`177` H. Bekker, H.J.C. Berendsen, E.J. Dijkstra, S. Achterop, R.
2491 v. Drunen, D. v. d. Spoel, A. Sijbers, and H. Keegstra
2492 *et al.*, "Gromacs Method of Virial Calculation Using a Single Sum"; pp.
2493 257–261 in *Physics computing 92*. Edited by R.A. de Groot and J.
2494 Nadrchal. World Scientific, Singapore, 1993.
2502 <div id="ref-Berendsen87">
2506 :sup:`178` H.J.C. Berendsen, J.R. Grigera, and T.P. Straatsma, "The
2507 missing term in effective pair potentials," *J. Phys. Chem.*, **91**
2516 <div id="ref-Gunsteren94a">
2518 .. _refGunsteren94a:
2520 :sup:`179` W.F. van Gunsteren and H.J.C. Berendsen, *Molecular dynamics
2521 of simple systems*, (1994).
2529 <div id="ref-RoethlisbergerQMMM">
2531 .. _refRoethlisbergerQMMM:
2533 :sup:`180` A. Laio, J. VandeVondele, U. Rothlisberger, *A Hamiltonian
2534 electrostatic coupling scheme for hybrid Car-Parrinello
2535 molecular dynamics simulations*, (2002).
2543 <div id="ref-GroenhofEwaldArtefact">
2545 .. _refGroenhofEwaldArtefact:
2547 :sup:`181` Hub, J. S., de Groot, B. L., Grubmüller, H., Groenhof, G.,
2548 "Quantifying artifacts in Ewald simulations of inhomogeneous systems with a net charge,"
2549 *J. Chem. Theory Comput.*, **10**, 381–390 (2014).
2557 <div id="ref-PallPairInteractions">
2559 .. _refPallPairInteractions:
2561 :sup:`182` Páll, S., Hess, B.,
2562 "A flexible algorithm for calculating pair interactions on SIMD architectures,"
2563 *Comput. Phys. Commun.*, **183**, 2641–2650 (2013).
2572 <div id="ref-Orzechowski2019">
2574 .. _refOrzechowski2008:
2576 :sup:`182` Orzechowski M, Tama F., "Flexible fitting of high-resolution x-ray
2577 structures into cryoelectron microscopy maps using biased molecular dynamics simulations",
2578 *Biophysical journal*, *95*, 5692–705, (2008).
2586 <div id="ref-Igaev2019">
2590 :sup:`183` Igaev, M., Kutzner, C., Bock, L. V., Vaiana, A. C., & Grubmüller, H.,
2591 "Automated cryo-EM structure refinement using correlation-driven molecular dynamics", *eLife*, **8**, e43542 (2019).
2599 <div id="ref-Bernetti2020">
2601 .. _refBernetti2020:
2603 :sup:`184` Bernetti, M. and Bussi, G.,
2604 "Pressure control using stochastic cell rescaling", *J. Chem. Phys.*, **153**, 114107 (2020).