StreaMD Documentation

StreaMD is a toolkit for high-throughput molecular dynamics simulations that automates preparation, equilibration, production, and analysis. It supports protein-only, protein-ligand, and protein-cofactor systems, can resume interrupted runs, and includes built-in analysis plus MM/PB(GB)SA and ProLIF tooling.

Contents

• Overview
  • Description
  • Next Steps
• Installation
  • Requirements
  • Install
  • Verify
• Input Preparation
  • Hydrogen Handling and Protonation
  • Target Preparation
  • Ligand Preparation (Optional)
  • Docking Procedure (Optional)
• Running Molecular Dynamics
  • Quick Start Examples
  • Command-Line Reference (run_md -h)
  • Standard Workflows
  • Replicas
  • Multi-Server Execution
  • Continue or Extend Simulations
  • GPU Usage
  • Custom MDP Files and Step Control
  • Boron-Containing Molecules (Gaussian)
  • Ligand-Binding Metalloproteins with MCPB.py
  • Additional Analysis Tools
• Advanced Features
  • Gaussian for Boron-Containing Molecules
  • MCPB.py for Metalloproteins
  • Custom MDP Files
  • Custom Force Field
  • StreaMD Step Control
  • Trajectory Size and Diagnostics
  • Parallelism and GPUs
• Outputs and Files
  • Logs
  • Directory Layout
  • Analysis Outputs
  • MD Outputs
• MM-PBSA/MM-GBSA Calculations
  • Usage
  • Examples
  • Outputs
• ProLIF (Protein-Ligand Interaction Fingerprints) Analysis
  • Usage
  • Examples
  • Effective Parallel Calculations
  • Outputs
  • Supplementary Scripts
• Trajectory Convergence Analysis
  • Usage
  • Examples
  • Outputs
• Configuration file
• Logging
• Changelog
• License
• Citation