OpenMMDL is an workflow, that allows an easy setup of OpenMM molecular dynamic simulations of protein-ligand complexes. OpenMMDL consists of:

OpenMMDL Setup - A webserver tool that allows to modify the Protein and generate Input Files for MD Simulations.

OpenMMDL Simulation - Performs a OpenMM MD Simulation with your Input files and further postprocesses the MD Simulation with MDTraj and MDAnalysis.

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

User guide:

• Installation
• 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

• OpenMMDL simulation functions
• OpenMMDL Analysis functions

Introduction

• Index

• Module Index

• Search Page