Molecular Dynamics Simulation with OpenMM

This repository contains a Python script for running molecular dynamics (MD) simulations using OpenMM. The code prepares a protein system, runs MD simulations, and calculates binding affinity between two chains (e.g., protein-peptide or protein-protein interactions) using MM/PBSA.

Features

• PDB Preparation: Fixes missing residues, atoms, and non-standard residues using PDBFixer.
• System Setup: Solvates the system, adds ions, and defines the force field (AMBER ff15ipq for protein and TIP3P for water).
• Simulation: Runs energy minimization, equilibration (NVT and NPT), and production MD simulations.
• GPU Support: Allows specifying which GPU to use for the simulation.
• Binding Affinity Calculation: Computes binding affinity between two chains (e.g., chain A and chain B) using MM/PBSA.

Requirements

• Python 3.7+
• OpenMM
• PDBFixer
• MDTraj
• NumPy

Install dependencies using:

pip install openmm pdbfixer mdtraj numpy

Usage

1. Place your input PDB file (e.g., complex.pdb) in the working directory.
2. Run the script:

   python md_simulation.py

3. The script will:
   • Prepare the PDB file.
   • Solvate the system and add ions.
   • Run energy minimization and equilibration.
   • Perform a production MD simulation.
   • Calculate binding affinity between two specified chains.

Customization

• Input PDB: Replace complex.pdb with your input PDB file.
• GPU Selection: Specify the GPU index in the setup_simulation function (default is 0).
• Chain Selection: Modify the chain selection strings in the calculate_binding_affinity function (e.g., "chainid 0" for chain A and "chainid 1" for chain B).

Output Files

• fixed_complex.pdb: Prepared and solvated PDB file.
• trajectory.dcd: Trajectory file from the production simulation.
• log.txt: Simulation logs (energy, temperature, volume, etc.).
• Binding affinity results printed to the console.

Example

To calculate binding affinity between chain A and chain B:

calculate_binding_affinity("trajectory.dcd", "solvated_complex.pdb", "chainid 0", "chainid 1")

License

This project is licensed under the MIT License. See the LICENSE file for details.