DEVELOPMENT VERSION of hop: Please note that this is a beta version of the package. It is still in heavy development. Feedback is very welcome (see below).
This is a collection of Python modules to analyze (primarily) water behaviour in MD simulations. The idea is to find regions with a density above a given threshold (hydration sites) and catalogue those sites. Once this is done, one can analyze water movement in terms of hops between those sites. The complicated solvation dynamics is thus represented as a graph in which hydration sites are the nodes (or vertices) and movements between sites are the edges.
Of course, it is also possible to look at the movement of other particles such as ions or small molecules --- one simply selects a different species.
The package is called 'Hop' (no clever acronym, just quick to type, and reflecting the fact that a "hopping analysis" is performed).
Hop requires MDAnalysis.
See the file INSTALL.rst for details.
The package is built on top of MDAnalysis, which typically needs to be installed beforehand.
Please see the contents of the doc/ directory, in particular
doc/overview.txt, and the Python doc strings.
Almost invariably, things will not work right away or it will be unclear how to accomplish a certain task. In order to keep track of feedback I ask you to use the Issue tracker at http://github.com/Becksteinlab/hop/issues
It helps tremendously to have everything in one place. Of course, feel free to also additionally email me directly.
Thanks!
If you use Hop in published work please cite (for the time being) the old abstract and the MDAnalysis paper (because Hop is built on top of MDAnalysis):
- Oliver Beckstein, Naveen Michaud-Agrawal and Thomas B. Woolf. Quantitative Analysis of Water Dynamics in and near Proteins. Biophysical Journal 96 (2009), 601a. doi:10.1016/j.bpj.2008.12.3147
- N Michaud-Agrawal, EJ Denning, TB Woolf, and O Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
Thanks!
Please do not hesitate to raise issues in the issue tracker or contact Oliver Beckstein <orbeckst@gmail.com> if problems occur or if you have suggestions how to improve the package or these instructions.