4.8.3. Water dynamics analysis — MDAnalysis.analysis.waterdynamics
- Author:
Alejandro Bernardin
- Year:
2014-2015
- Copyright:
GNU Public License v3
New in version 0.11.0.
This module provides functions to analyze water dynamics trajectories and water interactions with other molecules. The functions in this module are: water orientational relaxation (WOR) [Yeh1999], hydrogen bond lifetimes (HBL) [Rapaport1983], angular distribution (AD) [Grigera1996], mean square displacement (MSD) [Bródka1994] and survival probability (SP) [Liu2004].
For more information about this type of analysis please refer to [Araya-Secchi2014] (water in a protein cavity) and [Milischuk2011] (water in a nanopore).
References
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.
D.C. Rapaport. Hydrogen bonds in water. Molecular Physics, 50(5):1151–1162, 1983. doi:10.1080/00268978300102931.
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.
Aleksander Bródka. Diffusion in restricted volume. Molecular Physics, 82(5):1075–1078, 1994. doi:10.1080/00268979400100764.
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.
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.