| # 2AA-1-complete "Two Amino Acid" data set | |
| This folder contains a data set of all-atom molecular dynamics trajectories for all 400 | |
| dipeptides, i.e. small proteins composed of two amino acids. | |
| This includes also the peptides missing in the other 2AA datasets. | |
| Each peptide is simulated using classical molecular dynamics and the | |
| water is simulated using an implicit water model. | |
| For each protein 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: | |
| * 'time': `(T,)` array, simulation time in picoseconds. | |
| * '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. Construct initial protein using AmberTools's `tleap` program. | |
| 2. Process each PDB file using [pdbfixer](https://github.com/openmm/pdbfixer), | |
| adding all missing hydrogen atoms. This is the `state0.pdb` file. | |
| 3. For each all-atom PDB file, perform a molecular dynamics simulation: | |
| a.) Use OpenMM with the AMBER99 force field and implicit water model. | |
| b.) Perform an energy minimization (relaxation) from the initial extended | |
| configuration. | |
| c.) Use a second-order Langevin integrator at temperature to T=310K, | |
| friction=0.3/ps, timestep=1.0fs for 50,000 steps to equilibriate | |
| ("burn-in phase"). | |
| d.) Use a second-order Langevin integrator at temperature to T=310K, | |
| friction=0.3/ps, timestep=1.0fs for 5e6 steps to sample a trajectory | |
| ("sample phase"). | |
| 4. Save trajectory information to an `arrays.npz` file. | |
| 5. Shuffle and partition the trajectories into a `train` set | |
| (200 trajectories), `val` (80 trajectories), and `test` (100 trajectories). | |
| ## Credit and Authors | |
| This dataset was created in October 2022 as part of Timewarp. | |