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# 2AA-1-big "Two Amino Acid" data set
This folder contains a data set of all-atom molecular dynamics trajectories for all 380
of the 400 dipeptides, i.e. small proteins composed of two amino acids.
Each peptide is simulated using classical molecular dynamics and the
water is simulated using an implicit water model.
The trajectories are only saved every 10000 MD steps. There is no intermediate
spacing as for the other datasets for the Timewarp project.
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.
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