Simulation Data for "Solvent Treatment Inverts Methylation-Induced Structural Changes in BCL2 G-Quadruplex

This dataset contains simulation input files, analysis scripts, and processed data supporting the manuscript "Solvent Treatment Inverts Methylation-Induced Structural Changes in BCL2 G-Quadruplex: Evidence from Four Independent Computational Methods." CONTENTS Simulation Inputs:- GB-MD: AMBER input files (minimization, heating, production)- MetaD: PLUMED input file for well-tempered metadynamics- GaMD: Gaussian accelerated MD input files- MCMC: Mode Mixing MCMC configuration and core scripts Processed Data:- GB-MD: C4-C6 distance time series (100 ns, 10,000 frames per system)- MetaD: C4-C6 distance time series (200 ns per system)- GaMD: C4-C6 distance time series (200 ns per system)- MCMC: Summary statistics from 20 replicas per system Analysis Scripts:- convergence_analysis.py: Block averaging, autocorrelation, PMF convergence- create_figures.py: Figure generation for manuscript- cpptraj input files for distance calculations Structures:- Processed BCL2 G-quadruplex structure (PDB: 2F8U)- Methylation site definitions (C4, C6, C20) SYSTEMS STUDIED- Control (wild-type BCL2 G4)- C6-only (single methylation)- 3-site (C4+C6+C20 triple methylation) METHODS1. Mode Mixing MCMC (coarse-grained, implicit solvent)2. GB-MD with AMBER24 (all-atom, implicit solvent)3. Well-Tempered Metadynamics (all-atom, explicit solvent)4. Gaussian Accelerated MD (all-atom, explicit solvent)