| # 4AA-large "Four Amino Acid" data set, tetrapeptides | |
| The difference to the 4AA data set is the much longer simulation time. | |
| This folder contains a data set of all-atom molecular dynamics trajectories for | |
| 2333 tetrapeptides, i.e. small proteins composed of four amino acids. | |
| The data set is split into 1500 tetra-peptides in the train set, 400 in validation, and 433 in test. | |
| Each peptide in the train set is simulated for 50ns using classical molecular dynamics and the | |
| water is simulated using an implicit water model. Each other peptide is simulated for 500ns. | |
| 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 | |
| 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: | |
| 1. 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 1e8/1e9 steps to sample a trajectory ("sample phase"). | |
| 2. Save trajectory information every 10,000 steps (5ps) to an `arrays.npz` | |
| file. | |
| ## Credit and Authors | |
| This dataset was created in September 2022 as part of the Molecular Simulation | |
| initiative. | |