MolecularMinimumDistances

Documentation

Go to: https://m3g.github.io/MolecularMinimumDistances.jl

Introduction

This package computes the minimum distance between molecules, which are represented as arrays of coordinates in two or three dimensions.

To understand the utility and purpose of this package, consider the image below:

Here, there is one blue molecule, with 6 atoms, and several red molecules, with 2 atoms each. The package has identified which are the molecules of the red set that have at leat one atom within a cutoff from the atoms of the blue molecule, and annotated the corresponding atoms and the distances.

Features

• Fast and parallel cell-list approach, to compute minimum-distance for thousands, or millions of atoms.
• General periodic boundary conditions supported.
• Advanced mode for in-place calculations, for non-allocating iterative calls (for analysis of MD trajectories, for example).
• Modes for the calculation of minimum-distances in sets of molecules.

Citation

If this package was useful, please cite the article describing the main algorithms on which it is based:

L. Martínez, CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties within a cutoff. Computer Physics Communications, 279, 108452, 2022. https://doi.org/10.1016/j.cpc.2022.108452