First SimulationΒΆ
This is a good starting point for learning how to use OpenMM.
It loads a PDB file villin.pdb, which is the villin headpiece protein in a box of water. In then parameterizes it using the Amber14 forcefield and TIP3P-FB water model, energy minimizes it, and simulates it for 1000 steps with a langevin intergator.
[1]:
from openmm.app import *
from openmm import *
from openmm.unit import *
from sys import stdout
# Load in the PDB strucure
pdb = PDBFile('villin.pdb')
# Specifiy the forcefield
forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
# Combine the molecular topology and the forcefield
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
nonbondedCutoff=1*nanometer, constraints=HBonds)
# Create the integrator to use for advacing the equations of motion.
# It specifies a Langevin integrator.
# The paramters set are temperature, friction coefficient, and timestep.
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
# Combines the molecular topology, system, and integrator
# to begin a new simulation.
simulation = Simulation(pdb.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
# Perform local energy minimization
print("Minimizing energy...")
simulation.minimizeEnergy(maxIterations=100)
# Write the trajectory to a file called "output.pdb"
simulation.reporters.append(PDBReporter('output.pdb', 1000))
# Report infomation to the screen as the simulation runs
simulation.reporters.append(StateDataReporter(stdout, 100, step=True,
potentialEnergy=True, temperature=True))
#Run the simulation for 1000 timsteps
print("Running simulation...")
simulation.step(1000)
Minimizing energy...
Running simulation...
#"Step","Potential Energy (kJ/mole)","Temperature (K)"
100,-154191.66158040485,145.37797220666482
200,-150953.0689974915,201.0164460721387
300,-148544.29055599484,236.39454086545737
400,-146304.89286669478,257.74894083411374
500,-145158.8293928734,267.708432728178
600,-144177.68883101782,278.3559354737242
700,-143322.14100956134,284.5050593869164
800,-142675.28346424163,288.64843427235786
900,-142472.6888385688,293.79467976503724
1000,-142014.50850304624,291.9184722069045
