AD-3/README.md

Alanine Dipeptide trajectory data

This folder contains a minimal data set of two long MD trajectories for alanine dipeptide, the simplest dipeptide (22 atoms).

For each trajectory two files are available:

• protein-state0.pdb: contains the topology and initial 3D XYZ coordinates.
• protein-arrays.npz: contains trajectory information.

NPZ Information

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

1. For the included alanine-dipeptide.pdb PDB file, perform a molecular dynamics simulation: a.) Use OpenMM with the AMBER14 force field and implicit water model. 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 2e8 steps to sample a trajectory ("sample phase").
2. Save trajectory information every 1,000 steps (0.5ps) to an arrays.npz file.

Credit and Authors

This dataset was created in March 2022 as part of the Molecular Simulation initiative.