Data

Download materials

Course data lives in Course-MD-Data. Download it to COURSE_DIR/data by following the instructions in Setup.

Download alanine-dipeptide.pdb: minimal structure for OpenMM testing.
Download alanine-dipeptide-multi.pdb: multi-model PDB for trajectory analysis without DCD.
Download example_rmsd.csv: sample RMSD series for plots. To get the DCD, generate the trajectory locally (see Reference).

Protein-ligand complex data (OpenMM)

Download protein_orig.pdb: protein with ligand (for preparation).
Download protein.pdb: protein prepared for simulation.
Download ligand1.mol: ligand in MOL format.
Download ligand1.sdf: ligand in SDF format.

OpenMM data (python-examples)

The official OpenMM examples use input files you can download from the OpenMM repo. Store them in COURSE_DIR/data/openmm-examples for the Episode 2 scripts (Running simulations).

mkdir -p "$COURSE_DIR/data/openmm-examples"
base="https://raw.githubusercontent.com/openmm/openmm/master/examples/python-examples"
for file in \
  input.pdb input.inpcrd input.prmtop input.gro input.top \
  ala_ala_ala.pdb ala_ala_ala.psf charmm22.rtf charmm22.par \
  amoeba_solvated_phenol.xyz amoeba_phenol.prm amoebabio18.prm; do
  curl -L -o "$COURSE_DIR/data/openmm-examples/$file" "$base/$file"
done

Note: the Gromacs example requires access to force field files (includeDir). If you do not have them installed, use only the PDB/AMBER/CHARMM/Tinker examples.

Full DCD generator code

from openmm import app, unit
import openmm as mm

pdb = app.PDBFile('docs/data/alanine-dipeptide.pdb')
forcefield = app.ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')

modeller = app.Modeller(pdb.topology, pdb.positions)
modeller.addHydrogens(forcefield)

system = forcefield.createSystem(
    modeller.topology,
    nonbondedMethod=app.NoCutoff,
    constraints=app.HBonds
)

integrator = mm.LangevinIntegrator(
    300 * unit.kelvin,
    1.0 / unit.picosecond,
    2.0 * unit.femtoseconds
)

simulation = app.Simulation(modeller.topology, system, integrator)
simulation.context.setPositions(modeller.positions)

simulation.minimizeEnergy(maxIterations=100)
simulation.context.setVelocitiesToTemperature(300 * unit.kelvin)

simulation.reporters.append(app.DCDReporter('docs/data/alanine-dipeptide.dcd', 10))
simulation.step(200)

print('Wrote docs/data/alanine-dipeptide.dcd')

Script source: generate_example_dcd.py

Note: the command to generate the DCD is in Reference.