Creating a tutorial for performing Umbrella Sampling simulations with the wepy software package 

Voiceover

Presenter(s)(s)

Emma Fink

Abstract or Description

The determination of free-energy differences is a central task in computational (bio)chemistry, as this value is the driving force for chemical reactions. One software utilized for biomolecular simulations, wepy, is an open-source software framework for simulating rare events through weighted ensemble (WE) simulations. Wepy is written in pure Python, which readily allows alterations for development and testing of new methods or algorithms. With the addition of a two-atom Lennard-Jones pair based tutorial, wepy can now be more readily utilized for both weighted ensemble and umbrella sampling (US) simulations. While both methods do physical sampling of the (un)binding pathway, US differs from WE as it requires the addition of a potential energy term to the system, which is projected along a collective variable of interest. In this tutorial, we utilize the center-of-mass to center-of-mass (COM-COM) distance as the collective variable of choice, which is the feature of the system that helps to distinguish the progress of the reaction. Many simulations are run with a specific interval of COM-COM distances, and the data from these simulations is used to generate a free energy surface using the Weighted Histogram Analysis Method (WHAM). This is useful because it allows us to visualize the free energy landscape for a two molecule system, and to calculate (un)binding free energies. Our goal is to develop a tutorial to use Umbrella Sampling simulations to calculate the free energy for reactions with high energy barriers more efficiently.

Mentor

Alex Dickson, Nicole Roussey