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https://github.com/pritampanda15/molecular-dynamics
Self explained tutorial for molecular dynamics simulation using gromacs
https://github.com/pritampanda15/molecular-dynamics
charmm complex dynamics entropy freeenergy hpc hpc-clusters lipidbilayer molecular pca proteinligand simulation
Last synced: 24 days ago
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Self explained tutorial for molecular dynamics simulation using gromacs
- Host: GitHub
- URL: https://github.com/pritampanda15/molecular-dynamics
- Owner: pritampanda15
- Created: 2019-05-18T19:41:34.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2024-11-12T13:37:01.000Z (about 1 month ago)
- Last Synced: 2024-11-12T14:31:33.717Z (about 1 month ago)
- Topics: charmm, complex, dynamics, entropy, freeenergy, hpc, hpc-clusters, lipidbilayer, molecular, pca, proteinligand, simulation
- Language: Shell
- Homepage:
- Size: 9.19 MB
- Stars: 15
- Watchers: 3
- Forks: 6
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Molecular Dynamics with GROMACS
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.
## YouTube Tutorial Playlist
For a comprehensive guide, please refer to my [YouTube playlist on Molecular Dynamics with GROMACS](https://www.youtube.com/playlist?list=PLS3KFDv2o0CQIvkKuL7kU2rfowWIfHFFN).
---
## Table of Contents
- [Introduction](#introduction)
- [Getting Started](#getting-started)
- [Prerequisites](#prerequisites)
- [Installation](#installation)
- [Usage](#usage)
- [Preparing Input Files](#preparing-input-files)
- [Running Simulations](#running-simulations)
- [Analyzing Results](#analyzing-results)
- [Customization](#customization)
- [Links](#links)
- [Contributing](#contributing)
- [License](#license)
---
## Introduction
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.
## Getting Started
### Prerequisites
- **GROMACS**: Install GROMACS following the [official instructions](http://www.gromacs.org/Downloads).
- **Input Files**: You’ll need coordinate files (PDB or GRO format), force field parameters, and a simulation topology file (`.top`).
- **Topology File**: Prepare a `.top` file specifying molecule types and interactions in your system.
### Installation
Clone this repository to get started:
```bash
git clone https://github.com/yourusername/molecular-dynamics-gromacs.git
cd molecular-dynamics-gromacs
```
Ensure that GROMACS is installed and accessible in your system's PATH.
---
## Usage
### Preparing Input Files
1. **Coordinate File**: Contains atom positions in PDB or GRO format.
2. **Topology File**: Describes molecules and force field parameters.
3. **Parameter Files**: Any additional `.itp` force field files for specific molecules.
4. **Simulation Parameters**: Set up the `.mdp` file with parameters like time step, temperature control, and simulation duration.
### Running Simulations
1. **Edit `.mdp` File**: Customize the `.mdp` file with your desired simulation parameters.
2. **Generate a TPR File**: Create a GROMACS binary run input file (TPR):
```bash
gmx grompp -f simulation.mdp -c initial.gro -p system.top -o simulation.tpr
```
3. **Run Simulation**: Use `gmx mdrun` to start the simulation:
```bash
gmx mdrun -v -deffnm simulation
```
4. **Monitor Progress**: Check the log files to track simulation progress and address any issues.
### Analyzing Results
Use GROMACS analysis tools to extract and visualize simulation data:
- **Trajectory Visualization**: Use `gmx trjconv` for trajectory file conversions.
- **Data Analysis**: Compute properties like temperature, pressure, and radial distribution functions (RDF).
- **Plotting**: Visualize simulation results with your preferred plotting tools.
---
## Simulation Parameters
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
---
## Python Requirements
Make sure Python is installed with essential libraries for MD simulations:
```bash
pip install numpy scipy mdanalysis
```
Alternatively, use conda:
```bash
conda install numpy scipy mdanalysis
```
---
## Customization
To adjust simulation settings:
1. Modify the `.mdp` file for simulation-specific requirements.
2. Edit the topology file to add or remove molecular components.
3. Refer to [GROMACS documentation](http://www.gromacs.org/) for detailed customization options.
---
## Links
- [YouTube channel](https://youtu.be/hc8ZXbOMEfw)
- [Lipid Coordinates](https://people.ucalgary.ca/~tieleman/download.html)
- [Nanotube Generator](http://turin.nss.udel.edu/research/tubegenonline.html)
- [Ligand Topology Generator 1](http://www.swissparam.ch/)
- [CHARMM-GUI](https://www.charmm-gui.org/)
- [Topology File Generation](https://nptel.ac.in/courses/104101002/downloads/lecture-notes/module4/chapter35.pdf)
- [MD Tutorial with GROMACS](http://www.jyhuang.idv.tw/JYH_MDSimulation.html)
---
## Contributing
Contributions are welcome! To contribute:
1. Fork the repository and create a new branch.
2. Make your modifications.
3. Submit a pull request with a description of your changes.
Refer to the contribution guidelines for detailed information.
---
## License
This project is licensed under the [MIT License](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!**