Driver Repository

This is the Driver repository for our entire molecular dynamics and machine learning pipeline, providing a coordinated and seamless workflow for simulation, training, and analysis.

Overview

This repository contains scripts and tools that integrate multiple components of our computational pipeline:

• Regular OpenMM All Atom MD Programs and Scripts (openmm_generate)
  Standard molecular dynamics simulations using OpenMM for all-atom representations

• Training CGSchNet-based Models (base_model)
  Machine learning model training infrastructure for coarse-grained molecular representations using CGSchNet

• WESTPA for Data Generation (westpa_prop)
  Weighted Ensemble Simulation Toolkit with Parallelization and Analysis (WESTPA) integration supporting:

  • ML-driven simulations
  • Regular MD simulations
  • Custom progress coordinates
  • Enhanced sampling workflows

• Benchmark Suite (benchmark)
  Qualitative and quantitative comparison tools for evaluating and validating models

• Shared Modules (module)
  Repository containing all code and functions shared between base model, benchmark, openmm_generate, and westpa_prop.