GROMACS Workflows

This repository contains molecular dynamics workflows, trajectory analyses, and Python automation tools developed using GROMACS and Python.

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Current Project

10 ns Molecular Dynamics Simulation of 1HPV-Amprenavir Complex

System Information

• Protein: 1HPV
• Ligand: Amprenavir
• Simulation Length: 10 ns

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Molecular Dynamics Workflow

1. Protein preparation
2. Ligand topology generation
3. Solvation and ion addition
4. Energy minimization
5. NVT equilibration
6. NPT equilibration
7. Production MD simulation

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Analyses Performed

Structural Stability

• RMSD analysis
• Radius of gyration (Rg)

Interaction Analysis

• Radial Distribution Function (RDF)
• Hydrogen bond analysis

Surface Analysis

• Solvent Accessible Surface Area (SASA)

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Python Automation

Custom Python scripts were developed for:

• XVG parsing
• Automated scientific plotting
• Statistical analysis
• CSV export
• RDF/RMSD/MSD visualization

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Repository Structure

GROMACS-Workflows/
│
├── analysis/
│   ├── rmsd/
│   ├── rdf/
│   ├── sasa/
│   ├── hbonds/
│   └── gyration/
│
├── input_files/
├── scripts/
├── structures/
└── README.md

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Tools Used

• GROMACS
• Python
• NumPy
• Pandas
• Matplotlib
• Linux
• Git/GitHub

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Skills Demonstrated

• Molecular dynamics simulations
• Protein-ligand interaction analysis
• Scientific data analysis
• Python-based workflow automation
• Linux command-line workflows
• Computational chemistry techniques

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Future Improvements

• Automated batch analysis
• Publication-quality plotting
• Coordination number calculations
• TRAVIS-based trajectory analysis
• Diffusion coefficient analysis
• CO₂ capture simulation workflows