2. Background

hop is a collection of Python modules to analyze solvent dynamics in molecular dynamics (MD) simulations. It generates a spatially and temporally coarse grained representation of the dynamics in terms of a hopping graph.

The idea is to first find regions with a density above a given threshold and catalogue those sites (for water, these would be hydration sites, for other solvent molecules simply high density locations) . 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 hopping graph in which hydration sites are the nodes (or vertices) and movements between sites are the edges.

However, in principle one is not restricted to using high density sites. Any geometric partition of space can be used (such as “inside” and “outside” of a binding site to measure exchange with a binding site and derive on/off rate constants or “periplasmic” and “cytosolic” side of a membrane to derive permeation rates through a channel).