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,-156928.3664412292,119.42724365152638
200,-152702.44865222377,178.58521054689604
300,-149716.81507633877,218.70851263129916
400,-147636.2201801087,248.57551010078944
500,-145571.26717142982,258.9987338228007
600,-144681.64115660777,276.74360304344725
700,-143950.3796667094,282.6698998837718
800,-143059.2130492861,286.3311751586334
900,-142762.72032507005,294.2291290543645
1000,-142341.68001984924,293.62088757380496
