CodeEntropy: A Python Package for Multiscale Cell Correlation Entropy Estimation from Molecular Dynamics Simulations
References
- Henchman RH. Partition function for a simple liquid using cell theory parametrized by computer simulation. Journal of Chemical Physics. 2003;119:400–406. DOI: 10.1063/1.1578622
- Henchman RH. Free energy of liquid water from a computer simulation via cell theory. Journal of Chemical Physics. 2007;126:064504. DOI: 10.1063/1.2434964
- Higham J, Chou SY, Gräter F, Henchman RH. Entropy of flexible liquids from hierarchical force-torque covariance and coordination. Molecular Physics. 2018;116:1965–1976. DOI: 10.1080/00268976.2018.1459002
- Ali HS, Higham J, Henchman RH. Entropy of simulated liquids using multiscale cell correlation. Entropy. 2019;21:750. DOI: 10.3390/e21080750
- Irudayam SJ, Henchman RH. Solvation theory to provide a molecular interpretation of the hydrophobic entropy loss of noble-gas hydration. Journal of Physics: Condensed Matter. 2010;22:284108. DOI: 10.1088/0953-8984/22/28/284108
- Irudayam SJ, Plumb RD, Henchman RH. Entropic trends in aqueous solutions of the common functional groups. Faraday Discussions. 2010;145:467–485. DOI: 10.1039/B907383C
- Irudayam SJ, Henchman RH. Prediction and interpretation of the hydration entropies of monovalent cations and anions. Molecular Physics. 2011;109:37–48. DOI: 10.1080/00268976.2010.532162
- Gerogiokas G, Calabro G, Henchman RH, Southey MWY, Law RJ, Michel J. Prediction of small molecule hydration thermodynamics with grid cell theory. Journal of Chemical Theory and Computation. 2014;10:35–48. DOI: 10.1021/ct400783h
- Falcioni F, Kalayan J, Henchman RH. Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters. Journal of Computer-Aided Molecular Design. 2021;35:831–840. DOI: 10.1007/s10822-021-00401-w
- Ali HS, Henchman RH. Energy-entropy multiscale cell correlation method to predict toluene–water logP in the SAMPL9 challenge. Physical Chemistry Chemical Physics. 2023;25:27524–27531. DOI: 10.1039/D3CP03076H
- Hensen U, Gräter F, Henchman RH. Macromolecular entropy can be accurately computed from force. Journal of Chemical Theory and Computation. 2014;10:4777–4781. DOI: 10.1021/ct500684w
- Chakravorty A, Higham J, Henchman RH. Entropy of proteins using multiscale cell correlation. Journal of Chemical Information and Modeling. 2020;60:5540–5551. DOI: 10.1021/acs.jcim.0c00611
- Kalayan J, Chakravorty A, Warwicker J, Henchman RH. Total free energy analysis of fully hydrated proteins. Proteins. 2023;91:74–90. DOI: 10.1002/prot.26411
- Irudayam SJ, Henchman RH. Entropic cost of protein-ligand binding and its dependence on the entropy in solution. The Journal of Physical Chemistry B. 2009;113:5871–5884. DOI: 10.1021/jp809968p
- Kalayan J, Curtis RA, Warwicker J, Henchman RH. Thermodynamic origin of differential excipient-lysozyme interactions. Frontiers in Molecular Biosciences. 2021;8. DOI: 10.3389/fmolb.2021.689400
- Ali HS, Chakravorty A, Kalayan J, de Visser SP, Henchman RH. Energy-entropy method using Multiscale Cell Correlation to calculate binding free energies in the SAMPL8 Host-Guest Challenge. Journal of Computer-Aided Molecular Design. 2021;35:911–921. DOI: 10.1007/s10822-021-00406-5
- Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry. 2011;32:2319–2327. DOI: 10.1002/jcc.21787
- Gowers R, Linke M, Barnoud J, Reddy T, Melo M, Seyler S, et al. MDAnalysis: A python package for the rapid analysis of molecular dynamics simulations. Proceedings of the Python in Science Conference. 2016. DOI: 10.25080/majora-629e541a-00e
- Higham J, Henchman RH. Locally adaptive method to define coordination shell. Journal of Chemical Physics. 2016;145:084108. DOI: 10.1063/1.4961439
- Harris CR, Millman KJ, van der Walt SJ, Gommers R, Virtanen P, Cournapeau D, et al. Array programming with NumPy. Nature. 2020;585:357–362. DOI: 10.1038/s41586-020-2649-2
- Hagberg AA, Schult DA, Swart PJ. Exploring network structure, dynamics, and function using Networkx. In: Varoquaux G, Vaught T, Millman J, editors. Proceedings of the 7th Python in Science Conference. Pasadena, CA, USA; 2008. pp. 11–15. DOI: 10.25080/TCWV9851
- Dask Development Team. Dask: Library for dynamic task scheduling. Available from:
https://dask.org - Case DA, Babin V, Berryman JT, Betz RM, Cai Q, Cerutti DS, Cheatham TE
III. , Darden TA, Duke RE, Gohlke H, Goetz AW, Gusarov S, Homeyer N, Janowski P, Kaus J, Kolossváry I, Kovalenko A, Lee TS, LeGrand S, Luchko T, Luo R, Madej B, Merz KM, Paesani F, Roe DR, Roitberg A, Sagui C, Salomon-Ferrer R, Seabra G, Simmerling CL, Smith W, Swails J, Walker RC, Wang J, Wolf RM, Wu X, Kollman PA. Amber2014. San Francisco: University of California; 2014. - Wang JM, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general Amber force field. Journal of Computational Chemistry. 2004;25:1157–1174. DOI: 10.1002/jcc.20035
- Pascal TA, Lin ST, Goddard WA
III. . Thermodynamics of liquids: Standard molar entropies and heat capacities of common solvents from 2PT molecular dynamics. Physical Chemistry Chemical Physics. 2011;13:169–181. DOI: 10.1039/C0CP01549K - Amezcua M, Setiadi J, Ge Y, Mobley DL. An overview of the SAMPL8 host–guest binding challenge. Journal of Computer-Aided Molecular Design. 2022;36:707–734. DOI: 10.1007/s10822-022-00462-5
- Chakravorty A.
CodeEntropy . GitHub.https://github.com/arghya90/CodeEntropy - Kalayan J.
PoseidonBeta . GitHub.https://github.com/jkalayan/PoseidonBeta - Abraham M, Alekseenko A, Bergh C, Blau C, Briand E, Doijade M, et al. GROMACS 2023.3 Source code. Zenodo; 2023.
- Case DA, Betz RM, Cerutti DS, Cheatham TE
III. , Darden TA, Duke RE, Giese TJ, Gohlke H, Goetz AW, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee TS, LeGrand S, Li P, Lin C, Luchko T, Luo R, Mermelstein D, Merz KM, Monard G, Nguyen H, Nguyen HT, Omelyan I, Onufriev A, Roe DR, Roitberg A, Sagui C, Simmerling CL, Botello-Smith WM, Swails J, Walker RC, Wang J, Wolf RM, Wu X, Xiao L, Kollman PA. Amber2016. San Francisco: University of California; 2016. - Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics. 1983;79:926–935. DOI: 10.1063/1.445869
DOI: https://doi.org/10.5334/jors.741 | Journal eISSN: 2049-9647
Language: English
Page range: 55 - 55
Submitted on: May 13, 2026
Accepted on: Jul 7, 2026
Published on: Jul 20, 2026
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Keywords:
© 2026 Harry Swift, Jas Kalayan, Ioana A. Papa, Sarah K. Fegan, Richard H. Henchman, Sarah A. Harris, James Gebbie-Rayet, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.