Reproducibility Package for SimLab Science: Validated-Equivalence Experiments (DFT, Docking, and MD)

Abstract

This package contains the inputs, parameters, and platform-recorded reference outputs needed to reproduce the validated-equivalence experiments reported in the SimLab Science manuscript (submitted to the Journal of Computational Chemistry). SimLab Science is a browser-based platform for molecular dynamics, molecular docking, and quantum-chemical calculation; this package supports the manuscript's validation that the platform's orchestration layer does not alter the results obtained from running the same computational engines independently. It includes: (1) six ORCA input files for DFT geometry optimizations spanning neutral, anionic, cationic, and open-shell systems; (2) five protein-ligand complexes (1STP, 3PTB, 1HVR, 1HSG, 3ERT) with prepared receptor/ligand files, docking scripts, and AutoDock Vina execution logs; and (3) compiled GROMACS run inputs (.tpr) and recorded energy files for GPU-accelerated production MD of ribonuclease A at two timescales (20 ps and 1 ns). The SimLab Science platform itself is proprietary and is not included in this deposit; it remains freely accessible for evaluation at https://simlabscience.com. Each subfolder includes a README describing the exact steps needed to reproduce the corresponding table in the manuscript.