OpenMM.py

##########################################################################
# this script was generated by openmm-builder. to customize it further,
# you can save the file to disk and edit it with your favorite editor.
##########################################################################

from __future__ import print_function
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit
from sys import stdout

prmtop = app.AmberPrmtopFile('/home/burleyk/projects/sidechain/inputs/watDivaline.prmtop')
inpcrd = app.AmberInpcrdFile('/home/burleyk/projects/sidechain/inputs/watDivaline.inpcrd')

system = prmtop.createSystem(nonbondedMethod=app.PME, 
    nonbondedCutoff=1.0*unit.nanometers, constraints=app.HBonds, rigidWater=True, 
    ewaldErrorTolerance=0.0005)
integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picoseconds, 
    2.0*unit.femtoseconds)
integrator.setConstraintTolerance(0.00001)

platform = mm.Platform.getPlatformByName('CUDA')
properties = {'CudaPrecision': 'mixed'}
simulation = app.Simulation(prmtop.topology, system, integrator, platform, 
    properties)
simulation.context.setPositions(inpcrd.positions)

print('Minimizing...')
simulation.minimizeEnergy()

simulation.context.setVelocitiesToTemperature(300*unit.kelvin)
print('Equilibrating...')
simulation.step(100)

simulation.reporters.append(app.DCDReporter('trajectory.dcd', 1000))
simulation.reporters.append(app.StateDataReporter(stdout, 1000, step=True, 
    potentialEnergy=True, temperature=True, progress=True, remainingTime=True, 
    speed=True, totalSteps=1000, separator='\t'))

print('Running Production...')
simulation.step(1000000)
print('Done!')