About del_z_analysis.py

The Delta-Z Analysis for Peptide–Membrane Systems. This Python script performs batch Δz analysis between peptide COM and lipid headgroup COM from GROMACS .xvg files. It quantifies membrane penetration metrics (interface/core fractions, crossings) and classifies peptides as CPP-like or non-CPP. Results are automatically summarized into a CSV file for downstream analysis.

About tauoff_analyzer.py

The tauoff Contact Lifetime Analysis for Peptide–Membrane Interactions This script computes tauoff-based binding kinetics from GROMACS contact .xvg files using event-duration analysis and bootstrapped confidence intervals. It distinguishes reversible versus anchored contacts, generates per-peptide and global tauoff plots, and summarizes binding metrics in a CSV for comparative studies.

Per-Residue Contact Frequency Analysis

This script computes the per-residue contact frequency between a peptide/protein and membrane lipids (e.g., POPS) from GROMACS MD trajectories using MDAnalysis. Contacts are defined by a user-specified distance cutoff and summarized across the trajectory.

Key features: Residue-level contact detection Lipid headgroup–specific selections supported CSV output and bar plot visualization.

Per-Residue Protein–Membrane Interaction Energy Analysis

This script calculates time-averaged per-residue nonbonded interaction energies (Coulomb + Lennard–Jones) between a peptide/protein and membrane lipids using GROMACS trajectories. Only side-chain atoms are considered to avoid backbone and terminal artifacts.

Important This method reports interaction energies, not binding free energies.

Key features: Uses atomic charges directly from GROMACS .tpr topology Side-chain–only residue energy decomposition Mean and standard deviation per residue Energy bar plot