benchmark_foyer
This repository includes a few functions to evaluate the scaling of foyer's atom-typing and parametrization routines against a handful of variables, including system size, molecule size, and the use of a residue map.
Some code in this repository was used to generate Figure 4 in our manuscript about Foyer (see the paper or its corresponding pre-print).
Usage
First, install requirements
conda install --file requirements.txt && conda update --all
and then run the notebook
jupyter-notebook benchmark-foyer.ipynb
It should take on the order of an hour to run; some ranges in loops can be modified for shorter execution.