As mentioned in my last post, I am thrilled to have been accepted for Google Summer of Code 2025 with MDAnalysis and WESTPA. In this post, I am going to go deeper into the details of my project, which focuses on leveraging MDAnalysis trajectory streaming to perform on-the-fly analysis of multiple trajectories generated from Weighted Ensemble simulations.

Introduction to Weighted Ensemble Simulations

Weighted Ensemble simulations are a powerful technique in molecular dynamics that allow for efficient exploration of rare events and free energy landscapes. Weighted Ensemble methods are particularly appealing as they permit the calculation of kinetics and thermodynamics of complex processes without requiring the application of biasing potentials. In the Weighted Ensemble method, many short simulations are run in parallel. The simulations are run in iterations, where after each iteration, progress coordinates are calculated, and the simulations are duplicated or culled based on their progress. WESTPA (Weighted Ensemble Simulation Toolkit for Parallel Analysis) is state-of-the-art software for performing Weighted Ensemble simulations. It provides a framework for running and managing these simulations efficiently.

The Challenge of Analysis Overhead

A potential bottleneck in Weighted Ensemble simulations is the analysis step. After each iteration, the trajectory data needs to be loaded and the progress coordinates need to be calculated. Only once the progress coordinates have been calculated and sent to WESTPA can the next iteration of simulations be started. This can lead to significant delays, especially when the trajectories are short or many coordinates are calculated.

MDAnalysis Streaming: A Potential Solution

MDAnalysis is a powerful library for analyzing molecular dynamics simulations. A new feature in MDAnalysis is ability to stream a trajectory as the simulation is running. This means that the trajectory data can be processed in real-time, allowing for on-the-fly analysis. This feature is particularly useful if one wants to analyse processes that occur on very short timescales. Usually, the trajectory would have to be written to disk every few steps, which can lead to very large files when the simulations are long. By analysing the trajectory in real-time, we can avoid writing large files to disk and instead process the data as it is generated. MDAnalysis streaming is based upon Interactive Molecular Dynamics, which sends data from the simulation engine to an external program as the simulation is running.

Application to Weighted Ensemble Simulations

In this project, I aim to use MDAnalysis streaming to analyse the simulations as they are running. This will allow us to calculate the progress coordinates in real-time, eliminating the need to wait for the analysis step to complete before starting the next iteration of simulations. By integrating MDAnalysis streaming with WESTPA, we can significantly reduce the overhead associated with the analysis step in Weighted Ensemble simulations.