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.
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.
We welcome contributions, feature requests, and bug reports! Please use GitHub Issues to:
- Request new features
- Report bugs
- Suggest improvements
- Ask questions about the pipeline
Installation instructions will be added soon.
System requirements and dependencies will be listed here.
Instructions for setting up the computational environment will be added soon.
Quick start guide will be added as modules are released.
Step-by-step tutorials for common workflows will be provided soon.
Comprehensive documentation will be available soon.
License information will be added soon.