| # 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. | |