GROMACS: Molecular Dynamics Simulation

High-performance molecular dynamics simulation package for studying biomolecular systems with comprehensive analysis tools. GROMACS provides GPU-accelerated simulations with support for all major force fields (AMBER, CHARMM, GROMOS, OPLS-AA), enabling researchers to validate docking poses, study protein-ligand binding dynamics, and assess complex stability over nanosecond to microsecond timescales. The platform includes extensive trajectory analysis capabilities for RMSD, RMSF, energy calculations, and binding interaction monitoring essential for drug discovery validation.

Official Documentation: https://www.gromacs.org

Key Features

  • High-Performance MD: Optimized for speed and scalability
  • Force Field Support: AMBER, CHARMM, GROMOS, OPLS-AA
  • GPU Acceleration: CUDA and OpenCL support
  • Comprehensive Analysis: Built-in trajectory analysis tools

Simulation Workflow

Standard MD Protocol

  1. System Preparation: Structure processing and solvation
  2. Energy Minimization: Remove steric clashes
  3. Equilibration: NVT and NPT thermalization
  4. Production Run: Data collection simulation
  5. Analysis: Trajectory and property analysis

Key Settings

System Setup

  • Force Field: AMBER99SB-ILDN (recommended for proteins)
  • Water Model: TIP3P or SPC/E
  • Box Type: Dodecahedron for optimal efficiency
  • Ion Concentration: 0.15 M NaCl (physiological)

Simulation Parameters

  • Integration: md (leap-frog algorithm)
  • Time Step: 2 fs (with bond constraints)
  • Temperature: 300 K with V-rescale coupling
  • Pressure: 1 bar with Parrinello-Rahman coupling

Critical: Always perform adequate equilibration (NVT and NPT) before production runs to ensure system stability.

Integration Workflows

  • DiffDock results → GROMACS → Binding pose validation
  • Autodock Vina → GROMACS → Docking validation