This repository provides scripts and instructions for performing Molecular Dynamics (MD) simulations using GROMACS, a widely used software package for simulating atomic and molecular behavior. MD simulations allow for detailed exploration of biological molecules, materials, and chemical systems at the atomic level.
For a comprehensive guide, please refer to my YouTube playlist on Molecular Dynamics with GROMACS.
Molecular Dynamics (MD) with GROMACS enables you to model atomic interactions in different environments, such as solvated biomolecules or solid-state materials. This README provides step-by-step instructions for setting up and running MD simulations using GROMACS.
- GROMACS: Install GROMACS following the official instructions.
- Input Files: You’ll need coordinate files (PDB or GRO format), force field parameters, and a simulation topology file (
.top). - Topology File: Prepare a
.topfile specifying molecule types and interactions in your system.
Clone this repository to get started:
git clone https://github.com/yourusername/molecular-dynamics-gromacs.git
cd molecular-dynamics-gromacsEnsure that GROMACS is installed and accessible in your system's PATH.
- Coordinate File: Contains atom positions in PDB or GRO format.
- Topology File: Describes molecules and force field parameters.
- Parameter Files: Any additional
.itpforce field files for specific molecules. - Simulation Parameters: Set up the
.mdpfile with parameters like time step, temperature control, and simulation duration.
-
Edit
.mdpFile: Customize the.mdpfile with your desired simulation parameters. -
Generate a TPR File: Create a GROMACS binary run input file (TPR):
gmx grompp -f simulation.mdp -c initial.gro -p system.top -o simulation.tpr
-
Run Simulation: Use
gmx mdrunto start the simulation:gmx mdrun -v -deffnm simulation
-
Monitor Progress: Check the log files to track simulation progress and address any issues.
Use GROMACS analysis tools to extract and visualize simulation data:
- Trajectory Visualization: Use
gmx trjconvfor trajectory file conversions. - Data Analysis: Compute properties like temperature, pressure, and radial distribution functions (RDF).
- Plotting: Visualize simulation results with your preferred plotting tools.
Customize these key parameters in the .mdp file:
- Temperature & Pressure Control: Select an appropriate thermostat and barostat.
- Time Step: Use an integration time step suitable for your system’s dynamics.
- Force Field: Choose a force field that accurately describes your system’s interactions.
- Boundary Conditions: Define simulation cell boundaries (e.g., periodic boundary conditions).
- Simulation Length: Adjust simulation duration based on system needs.
Step Conversion:
- 1 ns = 500,000 steps
- 10 ns = 5,000,000 steps
- 100 ns = 50,000,000 steps
Make sure Python is installed with essential libraries for MD simulations:
pip install numpy scipy mdanalysisAlternatively, use conda:
conda install numpy scipy mdanalysisTo adjust simulation settings:
- Modify the
.mdpfile for simulation-specific requirements. - Edit the topology file to add or remove molecular components.
- Refer to GROMACS documentation for detailed customization options.
- YouTube channel
- Lipid Coordinates
- Nanotube Generator
- Ligand Topology Generator 1
- CHARMM-GUI
- Topology File Generation
- MD Tutorial with GROMACS
Contributions are welcome! To contribute:
- Fork the repository and create a new branch.
- Make your modifications.
- Submit a pull request with a description of your changes.
Refer to the contribution guidelines for detailed information.
This project is licensed under the MIT License. You are free to use, modify, and distribute this code for research and academic purposes.
Thank you for using this Molecular Dynamics with GROMACS repository! Feel free to reach out with questions or open an issue for any problems. Happy Simulating!