RhoGAP‑Aided GTP Hydrolysis in Small Rho GTPases (Classical and hybrid quantum–classical MD)

The MD_simulations folder contains Molecular Dynamics data, including AMBER topologies, compressed binary .xtc trajectories, and a .pdb file defining chains and residue IDs. The data are organized into three subfolders: REA, INT, and PROD, corresponding to the Reactant, Intermediate, and Product states, respectively. Each subfolder includes stripped topologies and trajectories for all system replicas. Solvent-free trajectories are downsampled to 2500 frames by retaining one frame every five from the original trajectories used in the analyses. The parm_files folder provides the input files required to build the AMBER topologies for the REA, INT, and PROD systems. The QMMM-MD folder is divided into two subfolders:(a) BOMDs, containing Born–Oppenheimer Molecular Dynamics data (AMBER topologies and .xtc trajectories), and(b) MTDs, containing metadynamics data (AMBER topologies, .xtc trajectories, and VMD visualization states). BOMD trajectories are solvent-free except for QM water molecules and are downsampled by retaining one frame every ten relative to the trajectories used for analysis. MTD trajectories are solvent-free except for QM water molecules W1, W2, and Wnuc (with W3 included in MTD4), and are downsampled by retaining one frame every twenty relative to the trajectories used for analysis.