Welcome to waterdynamics’s documentation!

This package provides classes and functions for the analysis of water dynamics and water interactions with other molecules in molecular simulations. The functions in this package are: water orientational relaxation (WOR) [1], hydrogen bond lifetimes (HBL) [2], angular distribution (AD) [3], mean square displacement (MSD) [4], and survival probability (SP) [5].

For more information about this type of analysis please refer to [6] (water in a protein cavity) and [7] (water in a nanopore).

Contents:

• Getting Started
  • Installation
• Examples
  • HydrogenBondLifetimes
  • WaterOrientationalRelaxation
  • AngularDistribution
  • MeanSquareDisplacement
  • SurvivalProbability
• Outputs
  • WaterOrientationalRelaxation
  • AngularDistribution
  • MeanSquareDisplacement
  • SurvivalProbability
• API Documentation
  • AngularDistribution
  • WaterOrientationalRelaxation
  • MeanSquareDisplacement
  • SurvivalProbability

Indices and tables

• Index

• Module Index

• Search Page

References

[1]

Yu-ling Yeh and Chung-Yuan Mou. Orientational relaxation dynamics of liquid water studied by molecular dynamics simulation. The Journal of Physical Chemistry B, 103(18):3699–3705, 1999. doi:10.1021/jp984584r.

[2]

D.C. Rapaport. Hydrogen bonds in water. Molecular Physics, 50(5):1151–1162, 1983. doi:10.1080/00268978300102931.

[3]

J. Raul Grigera, Susana G. Kalko, and Jorge Fischbarg. Wall−water interface. a molecular dynamics study. Langmuir, 12(1):154–158, 1996. doi:10.1021/la9408681.

[4]

Aleksander Bródka. Diffusion in restricted volume. Molecular Physics, 82(5):1075–1078, 1994. doi:10.1080/00268979400100764.

[5]

Pu Liu, Edward Harder, and B. J. Berne. On the calculation of diffusion coefficients in confined fluids and interfaces with an application to the liquid−vapor interface of water. The Journal of Physical Chemistry B, 108(21):6595–6602, 2004. doi:10.1021/jp0375057.

[6]

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.

[7]

Anatoli A. Milischuk and Branka M. Ladanyi. Structure and dynamics of water confined in silica nanopores. The Journal of Chemical Physics, 135(17):174709, 2011. doi:10.1063/1.3657408.