OpenMMDL is a workflow that enables the setup, simulation, and analysis of OpenMM molecular dynamics simulations of protein-ligand complexes. OpenMMDL consists of:

OpenMMDL Setup - A webserver tool that allows users to modify the protein and generate input files for MD simulations.

OpenMMDL Simulation - Runs an OpenMM MD simulation using the prepared input files and postprocesses the trajectory with MDTraj and MDAnalysis.

OpenMMDL Analysis - Analyzes protein-ligand interactions in OpenMM MD simulation trajectories.

User guide:

• Installation
• Release Notes
• Citation
• Frequently asked questions

OpenMMDL-Setup

• Running OpenMMDL Setup

OpenMMDL-Simulation

• Running OpenMMDL Simulation
  • Variables
  • Application
  • Running OpenMMDL Simulation test simulations
  • Running OpenMMDL Simulation using slurm
• OpenMMDL Simulation Output Files
  • Input Files
  • Checkpoints
  • MD Files
  • MD Postprocessing
  • Final Output

OpenMMDL-Analysis

• Running OpenMMDL Analysis
• OpenMMDL Analysis Output Files

Tutorials

• PDB Path
• Amber Path

API Docs

• API Documentation

Introduction

• Index

• Module Index

• Search Page