MATLAB Analysis Pipeline for Procrustes-Aligned Orientational Consistency Index (O_ij) and Positional Dynamics.

Zenodo Repository Description Integrated MD Trajectory Analysis Pipeline for Orientational Consistency (O_ij) and Positional Dynamics This repository provides the master MATLAB analysis pipeline and processed trajectory dataset used to evaluate residue-level orientational dynamics and conventional positional correlations from molecular dynamics (MD) simulations. The pipeline calculates and compares several complementary dynamical descriptors across multiple simulation systems and independent replicas. Key Features & Analysis Modules: Macrostructural & Convergence Profiling: Reads GROMACS output files (.xvg) to compute block-averaged RMSD, radius of gyration (Rg), potential/kinetic energies, and hydrogen-bonding profiles across production windows. Positional Metrics: Computes residue-residue Contact Frequency (CF_ij) and Dynamic Cross-Correlation Matrices (C_ij, DCCM) to capture spatial proximity and correlated Cartesian displacements. Orientational Consistency Pipeline (O_ij^0, O_ij, s_ij): Implements optimal 3D Procrustes rotational alignment via Singular Value Decomposition (SVD) on centered dipole unit vector trajectories. It calculates both unaligned projections (O_ij^0) and signed, scale-invariant orientational consistency (O_ij), parameterized by the mean directional sign factor (s_ij). Multi-Metric 2D Quadrant & Transition Cross-Analysis: Maps residue pairs across 2D parametric spaces (O_ij^0 vs. O_ij and C_ij vs. O_ij) using dual-threshold partitioning (0.5 cutoff) to identify non-contact orientational coupling (Quadrant Q2) and evaluate focal-residue partner networks. Intra- & Inter-System Consensus/Dissensus Framework: Classifies robust, conserved dynamical features versus state-dependent orientational fluctuations across independent replicas and system states based on mean and standard deviation thresholds. Usage & Requirements: Environment: MATLAB (R2023b or later recommended; requires Parallel Computing Toolbox for parfor acceleration). Execution: Run the master analysis script in the root directory containing the trajectory data structures and helper configuration functions (load_md_data.m). All processed matrices and summary statistics are automatically exported into integrated_upload.mat.