# Hop: analyzing solvent in molecular dynamics trajectories¶

Release: 0.4.0 Sep 20, 2018

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 is built with MDAnalysis.

Warning

This is legacy software that is provided “AS IS”. In particular, there are currently no tests and it is not guaranteed to work or produce correct results. Help and contributions are welcome!

hop is released under the GNU General Public License, v3 (because it links to MDAnalysis, which is GPL licensed).

## Documentation¶

The primary documentation consists of the online docs (which you are reading).

There is also some content in the doc/ directory, in particular doc/overview.txt.

## Bug reporting¶

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 https://github.com/Becksteinlab/hop/issues

## Citing¶

If you use Hop in published work please cite (for the time being) the abstract [Hop2009] and the MDAnalysis paper (because Hop is built on top of MDAnalysis) [MDAnalysis2011]. Thanks!

 [Hop2009] 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
 [MDAnalysis2011] N. Michaud-Agrawal, E. J. Denning, T. B. 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