FELBuilder | PCA + Free Energy Landscape Analysis Pipeline by Atharva Tilewale

About FELBuilder

Streamlining MD trajectory analysis for researchers

What is FELBuilder?

FELBuilder is an automated Python tool designed to simplify and streamline Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analysis from Molecular Dynamics (MD) trajectories.

It wraps GROMACS analysis commands into a single, user-friendly command-line interface (felbuilder), taking you from raw simulation files to publication-quality 2D and 3D FEL plots with a single command.

Key Features

Everything you need for efficient FEL analysis

Single-Command Execution

Runs the complete PCA–FEL workflow with one command. No need to manually chain multiple GROMACS tools.

Automated Indexing

Automatically generates a GROMACS index file for Protein + Ligand using the -g flag.

Organized Output

Consolidates all generated files into a single FEL_output directory for easy access.

Publication-Quality Plots

Produces high-quality 2D contour and 3D surface plots using Matplotlib, ready for your papers.

Smart Plot-Only Mode

Optionally skips analysis steps to plot directly from a .dat file when analysis is already done.

User-Friendly Interface

Colorful CLI, detailed help menu, and robust error handling for GROMACS operations.

Quick Start

Get started with FELBuilder in minutes

1

Install FELBuilder

Clone the repository and install dependencies

git clone https://github.com/AtharvaTilewale/FELBuilder.git
cd FELBuilder
pip install -r requirements.txt

2

Run Analysis

Execute FELBuilder with your MD trajectory files

# Basic usage
felbuilder -s topology.tpr -f trajectory.xtc

# With Protein + Ligand index generation
felbuilder -s topology.tpr -f trajectory.xtc -g

3

Get Your Plots

Find publication-ready 2D and 3D FEL plots in the FEL_output directory

FEL_output/
├── fel_2d_contour.png
├── fel_3d_surface.png
├── eigenval.xvg
├── proj.xvg
└── ...

Output Types

High-quality visualizations for your research

2D Contour Plot

Free energy landscape projected onto PC1 and PC2 with energy contours showing conformational states and transition barriers.

3D Surface Plot

Interactive 3D representation of the free energy surface for better visualization of energy minima and landscape topology.