File size: 1,663 Bytes
1558749 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 |
# 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.
|