Molecular Dynamics Trajectory Analysis

Practical — Research Master's Degree in Bioinformatics (Bio Data Analytics)
University of Manouba | Academic Year 2024–2025
Author: Rania Derouich

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Overview

This project provides a comprehensive analysis of a molecular dynamics (MD) simulation trajectory using Python and the pytraj library. The analysis covers key structural and thermodynamic metrics used to assess the stability, flexibility, and conformational dynamics of a protein system.

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Analyses Performed

Analysis	Metric	Description
RMSD	Root Mean Square Deviation	Global structural stability relative to initial frame
RMSF	Root Mean Square Fluctuation	Per-residue flexibility along the trajectory
Radius of Gyration	Rg	Compactness and folding state of the protein
Inter-residue Distance	Distance (Å)	Distance between first and last residues over time
PCA	Principal Component Analysis	Dominant conformational motions (Cα atoms)
Thermodynamic Properties	Temp, Volume, Pressure, Energy	System equilibration and stability

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Repository Structure

molecular-dynamics-analysis/
├── README.md
├── .gitignore
├── requirements.txt
├── molecular_dynamics_analysis.ipynb      # Full MD analysis pipeline
├── molecular_dynamics_analysis_v2.ipynb   # Refined version
└── data/                                  # ← Place your input files here (not tracked by git)
    ├── brad_dry.nc                        # MD trajectory (AMBER NetCDF) — not included
    └── topology_dry.prmtop               # Topology file (AMBER) — not included

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Input Data

File	Format	Description
data/brad_dry.nc	AMBER NetCDF	MD trajectory file
data/topology_dry.prmtop	AMBER	Topology file

Note: Raw trajectory and topology files are not included in this repository due to their large size. Place your own files in the data/ folder before running the notebooks.

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Setup & Usage

git clone https://github.com/your-username/molecular-dynamics-analysis.git
cd molecular-dynamics-analysis
pip install -r requirements.txt

Create the data/ folder and place your input files there:

data/
├── brad_dry.nc
└── topology_dry.prmtop

Then open a notebook and run all cells in order. The paths are already set to:

trajectory_file = 'data/brad_dry.nc'
topology_file   = 'data/topology_dry.prmtop'

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Requirements

• Python ≥ 3.10
• pytraj ≥ 2.0
• numpy ≥ 1.24
• matplotlib ≥ 3.7

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Technologies

Tool	Usage
pytraj	MD trajectory loading and analysis
NumPy	Numerical computing
Matplotlib	Visualization and plotting
AMBER format	Trajectory (.nc) & topology (.prmtop) input

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Author

Rania Derouich
Research Master's in Bioinformatics — Bio Data Analytics
University of Manouba, Tunisia

Academic project — 2024/2025