References

6. References#

[1]

B. J. Alder and T. E. Wainwright. Decay of the Velocity Autocorrelation Function. Physical Review A, 1(1):18–21, January 1970. URL: https://link.aps.org/doi/10.1103/PhysRevA.1.18 (visited on 2025-12-10), doi:10.1103/PhysRevA.1.18.

[2]

Michael P Allen, Dominic J Tildesley, and others. Computer simulation of liquids. 1987.

[3]

R. W. Balluffi, S. M. Allen, and W. C. Carter. Kinetics of Materials. Wiley-Interscience, 2005.

[4]

Arnaud Blondel and Martin Karplus. New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: elimination of singularities. Journal of computational chemistry, 17(9):1132–1141, 1996.

[5]

David Chandler. Introduction to Modern Statistical Mechanics. Oxford University Press, 1987.

[6]

Ken Dill and Sarina Bromberg. Molecular driving forces: statistical thermodynamics in biology, chemistry, physics, and nanoscience. Garland Science, 2010.

[7]

Donald L. Ermak and J. Andrew McCammon. Brownian dynamics with hydrodynamic interactions. The Journal of Chemical Physics, 69(4):1352–1360, 1978.

[8]

Daan Frenkel. Simulations: the dark side. The European Physical Journal Plus, 128(1):10, 2013.

[9]

Daan Frenkel and Berend Smit. Understanding molecular simulation. Elsevier, 1957.

[10]

Crispin W. Gardiner. Stochastic Methods: A Handbook for the Natural and Social Sciences. Springer Series in Synergetics, 2009.

[11]

Alan Grossfield, Paul N Patrone, Daniel R Roe, Andrew J Schultz, Daniel W Siderius, and Daniel M Zuckerman. Best practices for quantification of uncertainty and sampling quality in molecular simulations [article v1. 0]. Living journal of computational molecular science, 1(1):5067, 2018.

[12]

Jean-Pierre Hansen and Ian Ranald McDonald. Theory of simple liquids: with applications to soft matter. Elsevier/AP, Amstersdam, 4th edition edition, 2013. ISBN 978-0-12-387032-2.

[13]

William G. Hoover. Canonical dynamics: equilibrium phase-space distributions. Physical Review A, 31(3):1695–1697, 1985.

[14]

Michael P Howard, Antonia Statt, and Athanassios Z Panagiotopoulos. Note: smooth torsional potentials for degenerate dihedral angles. The Journal of chemical physics, 2017.

[15]

William L Jorgensen and Julian Tirado-Rives. The opls [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society, 110(6):1657–1666, 1988.

[16]

Charles Kittel and Paul McEuen. Introduction to solid state physics. John Wiley & Sons, 2018.

[17]

Kurt Kremer and Gary S Grest. Dynamics of entangled linear polymer melts: a molecular-dynamics simulation. The Journal of Chemical Physics, 92(8):5057–5086, 1990.

[18]

Ryogo Kubo. The fluctuation-dissipation theorem. Reports on Progress in Physics, 29(1):255–284, 1966.

[19]

David Landau and Kurt Binder. A guide to Monte Carlo simulations in statistical physics. Cambridge university press, 2021.

[20]

Benedict Leimkuhler and Charles Matthews. Robust and efficient configurational molecular sampling via langevin dynamics. The Journal of Chemical Physics, 138(17):174102, 2013.

[21]

J. E. Lennard-Jones. On the determination of molecular fields. Proceedings of the Royal Society A, 106(738):463–477, 1924. doi:10.1098/rspa.1924.0082.

[22]

Richard LeSar and Daryl C Chrzan. Is computational materials science overrated? Materials Today, 2(3):21–23, 1999.

[23]

Cameron Mackie, Alexander Zech, and Martin Head-Gordon. Effective two-body interactions. The Journal of Physical Chemistry A, 125(35):7750–7758, 2021.

[24]

Glenn J Martyna, Douglas J Tobias, and Michael L Klein. Constant pressure molecular dynamics algorithms. J. chem. Phys, 101(4177):10–1063, 1994.

[25]

Glenn J. Martyna, Michael L. Klein, and Mark E. Tuckerman. Nosé–hoover chains: the canonical ensemble via continuous dynamics. The Journal of Chemical Physics, 97(4):2635–2643, 1992.

[26]

Philip M. Morse. Diatomic molecules according to the wave mechanics. ii. vibrational levels. Physical Review, 34:57–64, 1929. doi:10.1103/PhysRev.34.57.

[27]

Shuichi Nosé. A molecular dynamics method for simulations in the canonical ensemble. Molecular Physics, 52(2):255–268, 1984.

[28]

Shuichi Nosé. A unified formulation of the constant temperature molecular dynamics methods. The Journal of Chemical Physics, 81(1):511–519, 1984.

[29]

Michele Parrinello and Aneesur Rahman. Polymorphic transitions in single crystals: a new molecular dynamics method. Journal of Applied physics, 52(12):7182–7190, 1981.

[30]

S Prasad, DL Mobley, E Braun, HB Mayes, JI Monroe, DM Zuckerman, and others. Best practices for foundations in molecular simulations [article v1. 0]. Living Journal of Computational Molecular Science, 1:1–28, 2018.

[31]

H. Risken. Fokker-planck equation: methods of solution and applications. Springer Series in Synergetics, 1996.

[32]

Christoph Scherer and Denis Andrienko. Understanding three-body contributions to coarse-grained force fields. Physical Chemistry Chemical Physics, 20(34):22387–22394, 2018.

[33]

Udo Seifert. Stochastic Thermodynamics. Cambridge University Press, 2025.

[34]

M Scott Shell. Thermodynamics and statistical mechanics: an integrated approach. Cambridge University Press, 2015.

[35]

Paulo CT Souza, Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grünewald, Ilias Patmanidis, Haleh Abdizadeh, Bart MH Bruininks, Tsjerk A Wassenaar, and others. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature methods, 18(4):382–388, 2021.

[36]

Antonia Statt. Mse 485: atomistic-scale simulations – statistical mechanics and ensembles. 2025. Course notes, University of Illinois at Urbana–Champaign.

[37]

Harry A Stern and Keith G Calkins. On mesh-based ewald methods: optimal parameters for two differentiation schemes. The Journal of chemical physics, 2008.

[38]

Masuo Suzuki. General theory of higher-order decomposition of exponential operators and symplectic integrators. Physics Letters A, 201(5-6):425–428, 1996.

[39]

A. Y. Toukmaji and J. A. Board. Ewald summation techniques in perspective: a survey. Computer Physics Communications, 95(2–3):73–92, 1996. doi:10.1016/0010-4655(96)00016-1.

[40]

Mark E Tuckerman, José Alejandre, Roberto López-Rendón, Andrea L Jochim, and Glenn J Martyna. A liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal–isobaric ensemble. Journal of Physics A: Mathematical and General, 39(19):5629, 2006.

[41]

Mark E Tuckerman and Glenn J Martyna. Understanding modern molecular dynamics: techniques and applications. 2000.

[42]

Mark E. Tuckerman. Statistical Mechanics: Theory and Molecular Simulation. Oxford University Press, 2010.

[43]

Mark E. Tuckerman. Statistical mechanics: theory and molecular simulation. Oxford University Press, 2010.

[44]

N. G. van Kampen. Stochastic Processes in Physics and Chemistry. North-Holland, 2007.

[45]

John D Weeks, David Chandler, and Hans C Andersen. Role of repulsive forces in determining the equilibrium structure of simple liquids. The Journal of Chemical Physics, 54(12):5237–5247, 1971.

[46]

M. Widom. Shape-adapted ewald summation. https://euler.phys.cmu.edu/widom/pubs/drafts/Dipole/dip.pdf.

[47]

Zhenhua Yao, Jian-Sheng Wang, Gui-Rong Liu, and Min Cheng. Improved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method. Computer physics communications, 161(1-2):27–35, 2004.

[48]

Haruo Yoshida. Construction of higher order symplectic integrators. Physics Letters A, 150(5-7):262–268, 1990.

[49]

Jan Zielkiewicz. Structural properties of water: comparison of the spc, spce, tip4p, and tip5p models of water. The Journal of chemical physics, 2005.

[50]

GROMACS development team. Gromacs reference manual: bonded interactions. https://manual.gromacs.org/current/reference-manual/functions/bonded-interactions.html, 2025.