Folding of villin miniprotein was studied by parallel tempering metadynamics driven by machine learning. To obtain a training set for machine learning, we generated a large series of structures of the protein by the de novo protein structure prediction package Rosetta. A neural network was trained to approximate the Rosetta score. Parallel tempering metadynamics driven by this approximated Rosetta score successfully predicted the native structure and the free energy surface of the studied system. These files make it possible to rerun all simulations. The directory METAD contains input files for metadynamics (no folding events observed). The directory PT-METAD contains input files for parallel tempering metadynamics. Lines with keywords METAD and PRINT in plumed.dat files are commented to accelerate automatic testing procedures. Uncomment these lines for a production run. All simulations were done using Gromacs 2016.4, Anncolvar 0.8, Plumed 2.4 and OpenMPI 4.0.0. METAD/ justcommands.sh - commands for running the simulation md.mdp - Gromacs input file with simulation parameters npt.cpt - Gromacs checkpoint file with high-resolution input structure npt.gro - Gromacs file with low-resolution input structure plumed.dat - Plumed input file with metadynamics options, uncomment commented METAD and PRINT lines for a production run ref.pdb - Reference structure for MOLINFO Plumed procedure ref2.pdb - Reference structure for FIT_TO_TEMPLATE Plumed procedure topol.top - Gromacs topology file PT-METAD/ justcommands.sh - commands for running the simulation md_0.mdp - md_42.mdp - Gromacs input files with simulation parameters (for different temperatures) nvt0.gro - nvt42.cpt - Gromacs checkpoint files with high-resolution input structures (for different temperatures) nvt0.gro - nvt42.gro - Gromacs files with low-resolution input structures (for different temperatures) plumed.dat - Plumed input file with metadynamics options, uncomment commented METAD and PRINT lines for a production run ref.pdb - Reference structure for MOLINFO Plumed procedure ref2.pdb - Reference structure for FIT_TO_TEMPLATE Plumed procedure topol.top - Gromacs topology file md5.log - MD5 signatures for files