Demo: Molecular Dynamics
MD Workflow

Ligand-X Demo

Demo: Molecular Dynamics

Experience the ease of setting up and running GPU-accelerated MD simulations with OpenMM in Ligand-X.

Video Walkthrough

Coming Soon: Video walkthrough demonstrating MD simulation setup in Ligand-X.

Data Flow Pipeline

When you submit an MD optimization job, your data flows through these stages:

1. Ligand Processing
  • Parse SDF/SMILES ligand
  • Generate 3D coordinates if needed
  • Assign AM1-BCC partial charges
  • Generate GAFF2/OpenFF force field parameters
2. System Building
  • Load and clean protein (PDBFixer)
  • Combine protein and ligand
  • Add TIP3P water box (1.0 nm padding)
  • Add ions (neutralize + 0.15 M ionic strength)
3. Energy Minimization
  • Steepest descent minimization
  • Remove steric clashes
  • Converge to local energy minimum
4. NVT Equilibration
  • Gradually heat system to 300 K
  • Velocity rescaling thermostat
  • Protein backbone restraints
  • 25,000 steps (50 ps)
5. NPT Equilibration
  • Monte Carlo barostat (1 bar)
  • Equilibrate box volume and density
  • Release restraints gradually
  • 25,000 steps (50 ps)
6. Output Generation
  • Extract final equilibrated coordinates
  • Write PDB files for each stage
  • Generate trajectory summary
Results
  • Equilibrated PDB structure
  • Energy plots (potential, kinetic, total)
  • System info (atoms, waters, ions, box size)
  • Trajectory file (DCD format, if production run)
  • Download options for all output files

Tools Used

Stage Tool Purpose
Ligand Prep RDKit Molecule parsing, 3D generation
Charges AmberTools AM1-BCC charge assignment
Force Fields OpenMMForceFields GAFF2, OpenFF parameters
Protein Prep PDBFixer Structure cleaning
Simulation OpenMM GPU-accelerated MD engine
Water Model TIP3P Explicit water solvation

Default Simulation Parameters

Parameter Default Description
temperature 300 K Target temperature
pressure 1.0 bar Target pressure
ionic_strength 0.15 M Salt concentration
min_steps 1000 Minimization steps
nvt_steps 25000 NVT equilibration (50 ps)
npt_steps 25000 NPT equilibration (50 ps)
protein_ff amber14-all Protein force field
ligand_ff gaff-2.11 Ligand force field

Output Files

File Description
minimized.pdb After energy minimization
nvt_equilibrated.pdb After NVT equilibration
npt_equilibrated.pdb After NPT equilibration
final.pdb Final equilibrated structure
trajectory.dcd Trajectory (if production run)

← Back to Ligand-X Learn the Theory →