MATLAB Workflow for MD Analysis: From Raw Signal Extraction (Center of Mass/Dipole) to Core Residue Identification via ACF Fitting

This repository provides a comprehensive MATLAB-based analytical framework for processing Molecular Dynamics (MD) trajectories. The workflow covers the entire pipeline, starting from raw signal extraction to the statistical identification of structural-dynamical hotspots (Core Residues).

Key Features:

1. Signal Processing: Extracts raw Center of Mass (CoM) and Dipole moment information from MD trajectories.

2. Metric Calculation: Computes proximity ($u$) and alignment ($m$) metrics to quantify residue-target interactions.

3. Dynamic Analysis: Calculates Autocorrelation Functions (ACF) for each metric to observe time-dependent decay.

4. Adaptive Fitting: Employs a bi-exponential fitting protocol to extract fast and slow relaxation times ($\tau_{f}, \tau_{s}$).

File Structure:

• Data Files (.mat): 4 initial files containing raw trajectory signals (Center of Mass and Dipole coordinates).

• Source Code (.m):

  • upload_01_Data.m: Processes raw signals to calculate $u, m$ metrics and generates the corresponding ACFs.

  • upload_02_ACF_Fitting.m: Performs the dual-metric adaptive fitting and to find final hotspots.

How to Use:

1. Place all .mat files and .m scripts in the same MATLAB working directory.

2. Execute upload_01_Data.m: first to generate the metric-based dataset.

3. Execute upload_02_ACF_Fitting.m to perform the dynamic analysis.