This repository contains scripts to analyse simulations of AOT using coarse-grained models. In order to use the JAX-accelerated version of the Willard-Chandler computation, install this fork of pytim: https://github.com/a-ws-m/pytim.
After installing this repo (pip install -e .), the analysis code can be
invoked using aot_cluster. Try aot_cluster -h for help on how to use the
code. It also requires a .yaml file that describes the cutoff distance and the
names of the tailgroups for the models you're analysing. An example for the
models described in the paper is in results.yaml. The path to the .tpr and
.xtc files needs to be changed to match your own simulation results.