TJ's attempt to run Lee-Ping's water model in OpenMM 5.1

run_water_sim.py

#!/usr/bin/env python

"""
Run a simple water simulation.
"""

from __future__ import print_function
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout

pdb = PDBFile('water512_mod.pdb')

forcefield = ForceField('iamoeba.xml')
#forcefield = ForceField('tip3p.xml')

system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, 
    nonbondedCutoff=0.7*nanometers, vdwCutoff=0.9*nanometer, 
    constraints=None, rigidWater=False) #,
    #polarization='direct', useDispersionCorrection=True)
integrator = LangevinIntegrator(300*kelvin, 1.0/picoseconds, 0.5*femtoseconds)
integrator.setConstraintTolerance(0.00001)

platform = Platform.getPlatformByName('CUDA')
properties = {'CudaPrecision': 'mixed', 'CudaDeviceIndex': '2'}
simulation = Simulation(pdb.topology, system, integrator, platform, properties)
simulation.context.setPositions(pdb.positions)

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

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

simulation.reporters.append(DCDReporter('output.dcd', 1000))
simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, 
    potentialEnergy=True, temperature=True))

print('Running Production...')
simulation.step(1000)
print('Done!')