This repository contains a collection of Molecular Dynamics (MD) simulation projects performed using GROMACS. The projects progress from a basic protein simulation in water to advanced protein–ligand simulations using different force fields and physiologically relevant ionic conditions.
The repository serves as a learning portfolio demonstrating the complete molecular dynamics workflow, including system preparation, topology generation, solvation, ion addition, equilibration, production simulations, and trajectory analysis.
protein-ligand-md-gromacs/
│
├── 01_Lysozyme_in_Water/
├── 02_Protein_Ligand_CHARMM36/
├── 03_Protein_Ligand_AMBER99SB/
├── 04_Protein_Ligand_charmm36_150mM/
│
├── .gitignore
└── README.md
| Project | Description |
|---|---|
| 01. Lysozyme in Water | Introduction to molecular dynamics simulation of lysozyme in an aqueous environment using GROMACS. |
| 02. Protein–Ligand (CHARMM36) | Protein–ligand molecular dynamics simulation using the CHARMM36 force field. |
| 03. Protein–Ligand (AMBER99SB) | Protein–ligand molecular dynamics simulation using the AMBER99SB force field. |
| 04. Protein–Ligand (CHARMM36, 150 mM NaCl) | Protein–ligand molecular dynamics simulation using the CHARMM36 force field under physiological ionic conditions (150 mM NaCl). |
- Molecular Dynamics (MD) Simulations
- Protein Structure Preparation
- Ligand Preparation
- CHARMM36 Force Field
- AMBER99SB Force Field
- Topology Generation
- Simulation Box Construction
- System Solvation
- Physiological Ion Addition (150 mM NaCl)
- Energy Minimization
- NVT Equilibration
- NPT Equilibration
- Production Molecular Dynamics
- Trajectory Analysis
- Root Mean Square Deviation (RMSD)
- Root Mean Square Fluctuation (RMSF)
- Radius of Gyration (Rg)
- Hydrogen Bond Analysis
- Solvent Accessible Surface Area (SASA)
- GROMACS 2023.3
- Ubuntu (WSL)
- PyMOL
- CGenFF
- Grace (xmgrace)
The projects include one or more of the following analyses:
- Temperature
- Pressure
- Density
- Root Mean Square Deviation (RMSD)
- Root Mean Square Fluctuation (RMSF)
- Radius of Gyration (Rg)
- Hydrogen Bond Analysis
- Solvent Accessible Surface Area (SASA)
- Complete GROMACS molecular dynamics workflows
- Protein and protein–ligand molecular dynamics simulations
- Multiple force fields (CHARMM36 & AMBER99SB)
- Physiological ionic environment (150 mM NaCl)
- Step-by-step simulation workflow
- Reproducible project organization
- Comprehensive trajectory analysis
Sawan Choudhary
M.Sc. Bioinformatics & Biotechnology
Chanakya University
⭐ This repository documents my learning journey in Molecular Dynamics Simulations using GROMACS, progressing from fundamental protein simulations to advanced protein–ligand systems under biologically relevant conditions.