{"id":21890586,"url":"https://github.com/pritampanda15/molecular-dynamics","last_synced_at":"2025-04-15T13:30:32.978Z","repository":{"id":50322359,"uuid":"187398571","full_name":"pritampanda15/Molecular-Dynamics","owner":"pritampanda15","description":"Self explained tutorial for molecular dynamics simulation using gromacs","archived":false,"fork":false,"pushed_at":"2024-11-16T12:45:26.000Z","size":32292,"stargazers_count":22,"open_issues_count":0,"forks_count":10,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-06T01:45:00.336Z","etag":null,"topics":["charmm","complex","dynamics","freeenergy","hpc","hpc-clusters","lipidbilayer","molecular","molecular-dynamics","molecular-dynamics-simulation","molecular-mechanics","molecular-simulation","pca","proteinligand","simulation"],"latest_commit_sha":null,"homepage":"","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pritampanda15.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-05-18T19:41:34.000Z","updated_at":"2025-04-05T16:52:22.000Z","dependencies_parsed_at":"2024-11-12T14:39:07.835Z","dependency_job_id":null,"html_url":"https://github.com/pritampanda15/Molecular-Dynamics","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pritampanda15%2FMolecular-Dynamics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pritampanda15%2FMolecular-Dynamics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pritampanda15%2FMolecular-Dynamics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pritampanda15%2FMolecular-Dynamics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pritampanda15","download_url":"https://codeload.github.com/pritampanda15/Molecular-Dynamics/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249079832,"owners_count":21209424,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["charmm","complex","dynamics","freeenergy","hpc","hpc-clusters","lipidbilayer","molecular","molecular-dynamics","molecular-dynamics-simulation","molecular-mechanics","molecular-simulation","pca","proteinligand","simulation"],"created_at":"2024-11-28T12:15:59.518Z","updated_at":"2025-04-15T13:30:32.955Z","avatar_url":"https://github.com/pritampanda15.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Molecular Dynamics with GROMACS\n\nThis 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.\n\n![GROMACS](https://github.com/pritampanda15/Molecular-Dynamics/blob/master/Youtube.png)\n\n## YouTube Tutorial Playlist\n\nFor a comprehensive guide, please refer to my [YouTube playlist on Molecular Dynamics with GROMACS](https://www.youtube.com/playlist?list=PLS3KFDv2o0CQIvkKuL7kU2rfowWIfHFFN).\n\n---\n\n## Table of Contents\n\n- [Introduction](#introduction)\n- [Getting Started](#getting-started)\n  - [Prerequisites](#prerequisites)\n  - [Installation](#installation)\n- [Usage](#usage)\n  - [Preparing Input Files](#preparing-input-files)\n  - [Running Simulations](#running-simulations)\n  - [Analyzing Results](#analyzing-results)\n- [Customization](#customization)\n- [Links](#links)\n- [Contributing](#contributing)\n- [License](#license)\n\n---\n\n## Introduction\n\nMolecular 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.\n\n## Getting Started\n\n### Prerequisites\n\n- **GROMACS**: Install GROMACS following the [official instructions](http://www.gromacs.org/Downloads).\n- **Input Files**: You’ll need coordinate files (PDB or GRO format), force field parameters, and a simulation topology file (`.top`).\n- **Topology File**: Prepare a `.top` file specifying molecule types and interactions in your system.\n\n### Installation\n\nClone this repository to get started:\n\n```bash\ngit clone https://github.com/yourusername/molecular-dynamics-gromacs.git\ncd molecular-dynamics-gromacs\n```\n\nEnsure that GROMACS is installed and accessible in your system's PATH.\n\n---\n\n## Usage\n\n### Preparing Input Files\n\n1. **Coordinate File**: Contains atom positions in PDB or GRO format.\n2. **Topology File**: Describes molecules and force field parameters.\n3. **Parameter Files**: Any additional `.itp` force field files for specific molecules.\n4. **Simulation Parameters**: Set up the `.mdp` file with parameters like time step, temperature control, and simulation duration.\n\n### Running Simulations\n\n1. **Edit `.mdp` File**: Customize the `.mdp` file with your desired simulation parameters.\n2. **Generate a TPR File**: Create a GROMACS binary run input file (TPR):\n\n   ```bash\n   gmx grompp -f simulation.mdp -c initial.gro -p system.top -o simulation.tpr\n   ```\n\n3. **Run Simulation**: Use `gmx mdrun` to start the simulation:\n\n   ```bash\n   gmx mdrun -v -deffnm simulation\n   ```\n\n4. **Monitor Progress**: Check the log files to track simulation progress and address any issues.\n\n### Analyzing Results\n\nUse GROMACS analysis tools to extract and visualize simulation data:\n\n- **Trajectory Visualization**: Use `gmx trjconv` for trajectory file conversions.\n- **Data Analysis**: Compute properties like temperature, pressure, and radial distribution functions (RDF).\n- **Plotting**: Visualize simulation results with your preferred plotting tools.\n\n---\n\n## Simulation Parameters\n\nCustomize these key parameters in the `.mdp` file:\n\n- **Temperature \u0026 Pressure Control**: Select an appropriate thermostat and barostat.\n- **Time Step**: Use an integration time step suitable for your system’s dynamics.\n- **Force Field**: Choose a force field that accurately describes your system’s interactions.\n- **Boundary Conditions**: Define simulation cell boundaries (e.g., periodic boundary conditions).\n- **Simulation Length**: Adjust simulation duration based on system needs.\n\n\u003e **Step Conversion**:\n\u003e - 1 ns = 500,000 steps\n\u003e - 10 ns = 5,000,000 steps\n\u003e - 100 ns = 50,000,000 steps\n\n---\n\n## Python Requirements\n\nMake sure Python is installed with essential libraries for MD simulations:\n\n```bash\npip install numpy scipy mdanalysis\n```\n\nAlternatively, use conda:\n\n```bash\nconda install numpy scipy mdanalysis\n```\n\n---\n\n## Customization\n\nTo adjust simulation settings:\n\n1. Modify the `.mdp` file for simulation-specific requirements.\n2. Edit the topology file to add or remove molecular components.\n3. Refer to [GROMACS documentation](http://www.gromacs.org/) for detailed customization options.\n\n---\n\n## Links\n\n- [YouTube channel](https://youtu.be/hc8ZXbOMEfw)\n- [Lipid Coordinates](https://people.ucalgary.ca/~tieleman/download.html)\n- [Nanotube Generator](http://turin.nss.udel.edu/research/tubegenonline.html)\n- [Ligand Topology Generator 1](http://www.swissparam.ch/)\n- [CHARMM-GUI](https://www.charmm-gui.org/)\n- [Topology File Generation](https://nptel.ac.in/courses/104101002/downloads/lecture-notes/module4/chapter35.pdf)\n- [MD Tutorial with GROMACS](http://www.jyhuang.idv.tw/JYH_MDSimulation.html)\n\n---\n\n## Contributing\n\nContributions are welcome! To contribute:\n\n1. Fork the repository and create a new branch.\n2. Make your modifications.\n3. Submit a pull request with a description of your changes.\n\nRefer to the contribution guidelines for detailed information.\n\n---\n\n## License\n\nThis project is licensed under the [MIT License](LICENSE). You are free to use, modify, and distribute this code for research and academic purposes.\n\n---\n\nThank 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!**\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpritampanda15%2Fmolecular-dynamics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpritampanda15%2Fmolecular-dynamics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpritampanda15%2Fmolecular-dynamics/lists"}