4AA-huge "Four Amino Acid" data set, tetrapeptides

This folder contains a data set of all-atom molecular dynamics trajectories for tetrapeptides, i.e. small proteins composed of four amino acids. The data set contains mostly validation and test trajectories as it was mostly used to validation and test purposes. The training trajectories used are usually shorter. Each peptide is simulated for 1 micros second using classical molecular dynamics and the water is simulated using an implicit water model.

For each trajectory two files are available:

protein-state0.pdb: contains the topology and initial 3D XYZ coordinates.
protein-arrays.npz: contains trajectory information.
protein-time.npy: contains the wall-clock simulation time.

NPZ Information

Each NPZ file contains detailed information for a subset of simulation steps. There are T such frames and each NPZ file contains the following arrays:

'step': (T,) array, Md step number.
'energies': (T,2) array, each row containing [potential, kinetic] energies in kJ/mol.
'positions': (T,num_atoms,3) array, positions in nm.
'velocities': (T,num_atoms,3) array, velocities in nm/ps.
'forces': (T,num_atoms,3) array, forces in kJ/(mol nm).

Dataset construction

The dataset was constructed in the following way:

For all included PDB files, perform a molecular dynamics simulation:

a.) Use OpenMM with the AMBER14 force field and implicit water (preset=amber14-implicit).`

b.) Perform an energy minimization (relaxation) from the initial PDB configuration. c.) Use a Langevin integrator at temperature T=310K, friction=0.3/ps, timestep=0.5fs for 2e6 steps to equilibriate ("burn-in phase"). d.) Use a Langevin integrator at temperature T=310K, friction=0.3/ps, timestep=0.5fs for 5e5 steps to sample a trajectory ("sample phase").
Save trajectory information every 1,000 steps (0.5ps) to an arrays.npz file.

Credit and Authors

This dataset was created in Oktober 2022 as part of the Timewarp project