from openmm.app import *
from openmm import *
from openmm.unit import *
from sys import stdout

inpcrd = AmberInpcrdFile('input.inpcrd')
prmtop = AmberPrmtopFile('input.prmtop', periodicBoxVectors=inpcrd.boxVectors)
system = prmtop.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
simulation = Simulation(prmtop.topology, system, integrator)
simulation.context.setPositions(inpcrd.positions)
simulation.minimizeEnergy()
simulation.reporters.append(DCDReporter('output.dcd', 1000))
simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True))
simulation.step(10000)
