13.2.11. Correlations utilities — MDAnalysis.lib.correlations

Authors:

Paul Smith & Mateusz Bieniek

Year:

2020

Copyright:

GNU Public License v2

New in version 1.0.0.

This module is primarily for internal use by other analysis modules. It provides functionality for calculating the time autocorrelation function of a binary variable (i.e one that is either true or false at each frame for a given atom/molecule/set of molecules). This module includes functions for calculating both the time continuous autocorrelation and the intermittent autocorrelation. The function autocorrelation() calculates the continuous autocorrelation only. The data may be pre-processed using the function intermittency() in order to acount for intermittency before passing the results to autocorrelation().

This module is inspired by seemingly disparate analyses that rely on the same underlying calculation, including the survival probability of water around proteins [Araya-Secchi2014], hydrogen bond lifetimes [Gowers2015, Araya-Secchi2014], and the rate of cholesterol flip-flop in lipid bilayers [Gu2019].

See also

Analysis tools that make use of modules:

  • MDAnalysis.analysis.waterdynamics.SurvivalProbability

    Calculates the continuous or intermittent survival probability of an atom group in a region of interest.

  • MDAnalysis.analysis.hbonds.hbond_analysis

    Calculates the continuous or intermittent hydrogen bond lifetime.

References

[Gowers2015] (1,2)

Richard J. Gowers and Paola Carbone. A multiscale approach to model hydrogen bonding: the case of polyamide. The journal of Chemical Physics, 142(22):224907, 2015. doi:10.1063/1.4922445.

[Araya-Secchi2014] (1,2,3)

Raul Araya-Secchi, Tomas Perez-Acle, Seung-gu Kang, Tien Huynh, Alejandro Bernardin, Yerko Escalona, Jose-Antonio Garate, Agustin D. Martínez, Isaac E. García, Juan C. Sáez, and Ruhong Zhou. Characterization of a novel water pocket inside the human cx26 hemichannel structure. Biophysical Journal, 107(3):599–612, 2014. doi:10.1016/j.bpj.2014.05.037.

[Gu2019]

Ruo-Xu Gu, Svetlana Baoukina, and D. Peter Tieleman. Cholesterol flip-flop in heterogeneous membranes. Journal of Chemical Theory and Computation, 15(3):2064–2070, 2019. doi:10.1021/acs.jctc.8b00933.