Code for paper: Exploring Entropy Landscapes using Hard Particle Metadynamics

In paper, Exploring Entropy Landscapes using Hard Particle Metadynamics, we introduce a new algorithm that integrates the Hard Particle Monte Carlo scheme with Metadynamics, which we term "HPMetaD".

To perform HPMetaD simulations, we implemented the algorithm as a HOOMD-blue custom updater, and we provide a minimal example in this repository:

simulation.ipynb - HPMetaD simulation of N = 50 $S_2$ particles (see paper for shape definition).

colvar.py – Implementation of several commonly used order parameters, used in hpmetad.py. Modify this file to include custom collective variables.

hpmetad.py – Implementation of the HPMetaD algorithm.

restart.ipynb - Restart and continue the HPMetaD simulation.

analysis.ipynb - Analyze the simulation data for, e.g., checking the acceptance rate, collective variable/bia potential vs time, and plotting the free energy profile.

In the larger_system_data directory, we also provide a simulation trajectory with N = 500 $S_2$ particles (run 5 as labeled in the Supplementary Material). The rest of the simulation data for our paper can be provided upon request.