Bibliography

[1]

William Humphrey, Andrew Dalke, and Klaus Schulten. VMD: visual molecular dynamics. Journal of molecular graphics, 14(1):33–38, 1996.

[2]

Guido Van Rossum and Fred L Drake Jr. Python reference manual. Centrum voor Wiskunde en Informatica Amsterdam, 1995.

[3]

Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, and Oliver Beckstein. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of computational chemistry, 32(10):2319–2327, 2011.

[4]

Richard J Gowers, Max Linke, Jonathan Barnoud, Tyler JE Reddy, Manuel N Melo, Sean L Seyler, Jan Domanski, David L Dotson, Sébastien Buchoux, Ian M Kenney, and others. MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations. In Proceedings of the 15th python in science conference, volume 98, 105. SciPy Austin, TX, 2016.

[5]

Daan Frenkel and Berend Smit. Understanding molecular simulation: from algorithms to applications. Elsevier, 2023.

[6]

Michael P Allen and Dominic J Tildesley. Computer simulation of liquids. Oxford university press, 2017.

[7]

Jean-Louis Barrat and Jean-Pierre Hansen. Basic concepts for simple and complex liquids. Cambridge University Press, 2003.

[8]

Jean-Pierre Hansen and Ian Ranald McDonald. Theory of simple liquids: with applications to soft matter. Academic press, 2013.

[9]

Hendrik Antoon Lorentz. Ueber die anwendung des satzes vom virial in der kinetischen theorie der gase. Annalen der physik, 248(1):127–136, 1881.

[10]

Daniel Berthelot. Sur le mélange des gaz. Compt. Rendus, 126(3):15, 1898.

[11]

T Schneider and E Stoll. Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions. Physical Review B, 17(3):1302, 1978.

[12]

Herman JC Berendsen, JPM van Postma, Wilfred F Van Gunsteren, ARHJ DiNola, and Jan R Haak. Molecular dynamics with coupling to an external bath. The Journal of chemical physics, 81(8):3684–3690, 1984.

[13]

Peter Debye. Näherungsformeln für die zylinderfunktionen für große werte des arguments und unbeschränkt veränderliche werte des index. Mathematische Annalen, 67(4):535–558, 1909.

[14]

Giovanni Bussi, Davide Donadio, and Michele Parrinello. Canonical sampling through velocity rescaling. The Journal of chemical physics, 2007.

[15]

Tom Darden, Darrin York, and Lee Pedersen. Particle mesh ewald: an n⋅ log (n) method for ewald sums in large systems. The Journal of chemical physics, 98(12):10089–10092, 1993.

[16]

Ulrich Essmann, Lalith Perera, Max L Berkowitz, Tom Darden, Hsing Lee, and Lee G Pedersen. A smooth particle mesh ewald method. The Journal of chemical physics, 103(19):8577–8593, 1995.

[17]

Berk Hess, Henk Bekker, Herman JC Berendsen, and Johannes GEM Fraaije. Lincs: a linear constraint solver for molecular simulations. Journal of computational chemistry, 18(12):1463–1472, 1997.

[18]

Mattia Bernetti and Giovanni Bussi. Pressure control using stochastic cell rescaling. The Journal of Chemical Physics, 2020.

[19]

JH Simpson and HY Carr. Diffusion and nuclear spin relaxation in water. Physical Review, 111(5):1201, 1958.

[20]

Philip Loche, Patrick Steinbrunner, Sean Friedowitz, Roland R Netz, and Douwe Jan Bonthuis. Transferable ion force fields in water from a simultaneous optimization of ion solvation and ion–ion interaction. The Journal of Physical Chemistry B, 125(30):8581–8587, 2021.

[21]

Protein Data Bank. Protein data bank. Nature New Biol, 233(223):10–1038, 1971.

[22]

Gary S Shaw, Robert S Hodges, and Brian D Sykes. Determination of the solution structure of a synthetic two-site calcium-binding homodimeric protein domain by nmr spectroscopy. Biochemistry, 31(40):9572–9580, 1992.

[23]

Herman-J-C Berendsen, J-Raúl Grigera, and Tjerk P Straatsma. The missing term in effective pair potentials. Journal of Physical Chemistry, 91(24):6269–6271, 1987.

[24]

Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, and others. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of computational chemistry, 24(16):1999–2012, 2003.

[25]

Susanne Liese, Manuel Gensler, Stefanie Krysiak, Richard Schwarzl, Andreas Achazi, Beate Paulus, Thorsten Hugel, Jürgen P Rabe, and Roland R Netz. Hydration effects turn a highly stretched polymer from an entropic into an energetic spring. ACS nano, 11(1):702–712, 2017.

[26]

Kurt Binder. Monte Carlo and molecular dynamics simulations in polymer science. Oxford University Press, 1995.

[27]

Raúl Fuentes-Azcatl and José Alejandre. Non-polarizable force field of water based on the dielectric constant: tip4p/$\varepsilon $. The Journal of Physical Chemistry B, 118(5):1263–1272, 2014.

[28]

Alpeshkumar K Malde, Le Zuo, Matthew Breeze, Martin Stroet, David Poger, Pramod C Nair, Chris Oostenbrink, and Alan E Mark. An automated force field topology builder (ATB) and repository: version 1.0. Journal of chemical theory and computation, 7(12):4026–4037, 2011.

[29]

Ethan Stewart, Roseanne L Shields, and Ramona S Taylor. Molecular dynamics simulations of the liquid/vapor interface of aqueous ethanol solutions as a function of concentration. The Journal of Physical Chemistry B, 107(10):2333–2343, 2003.

[30]

Jose LF Abascal and Carlos Vega. A general purpose model for the condensed phases of water: TIP4P/2005. The Journal of chemical physics, 2005.