TestReplicaExchangeSampler.py

from openmm import *
from openmm.app import *
from openmm.unit import *
import numpy as np
import unittest

class TestReplicaExchangeSampler(unittest.TestCase):
    def testTemperature(self):
        """Test a set of replicas that differ in temperature."""
        system = System()
        system.addParticle(1.0)
        force = CustomExternalForce('x*x+y*y+z*z')
        force.addParticle(0)
        system.addForce(force)
        states = [{'temperature':t*kelvin} for t in np.geomspace(300.0, 600.0, 5)]
        for reinitialize in [False, True]:
            integrator = LangevinIntegrator(300*kelvin, 10/picosecond, 0.01*picosecond)
            simulation = Simulation(Topology(), system, integrator, Platform.getPlatform('Reference'))
            repex = ReplicaExchangeSampler(states, simulation, 20, reinitialize)
            energies = [0.0*kilojoules_per_mole]*len(states)
            exchanged = False

            def recordEnergies(repex):
                if repex.replicaStateIndex != list(range(len(states))):
                    nonlocal exchanged
                    exchanged = True
                for i in range(len(states)):
                    simulation.context.setState(repex.replicaConformation[i])
                    energies[repex.replicaStateIndex[i]] += simulation.context.getState(energy=True).getPotentialEnergy()

            repex.reporters.append(recordEnergies)
            for i in range(len(states)):
                repex.simulateReplica(i, 100)
            steps = 1000
            repex.simulate(steps)
            self.assertTrue(exchanged)
            for i, e in enumerate(energies):
                average = e/steps
                expected = 1.5*(states[i]['temperature']*MOLAR_GAS_CONSTANT_R)
                self.assertTrue(0.7 < average/expected < 1.3)
                self.assertEqual(steps*20+100, repex.replicaConformation[i].getStepCount())

    def testParameter(self):
        """Test a set of replicas that differ in a force parameter."""
        system = System()
        system.addParticle(1.0)
        force = CustomExternalForce('0.5*k*x*x')
        force.addGlobalParameter('k', 1.0)
        force.addParticle(0)
        system.addForce(force)
        states = [{'k':k*kilojoules_per_mole/(nanometer**2)} for k in np.geomspace(5.0, 100.0, 5)]
        for reinitialize in [False, True]:
            integrator = LangevinIntegrator(300*kelvin, 10/picosecond, 0.01*picosecond)
            simulation = Simulation(Topology(), system, integrator, Platform.getPlatform('Reference'))
            repex = ReplicaExchangeSampler(states, simulation, 20, reinitialize)
            r2 = [0.0*nanometer**2]*len(states)
            exchanged = False

            def recordDisplacements(repex):
                if repex.replicaStateIndex != list(range(len(states))):
                    nonlocal exchanged
                    exchanged = True
                for i in range(len(states)):
                    x = repex.replicaConformation[i].getPositions()[0][0]
                    r2[repex.replicaStateIndex[i]] += x*x

            repex.reporters.append(recordDisplacements)
            for i in range(len(states)):
                repex.simulateReplica(i, 100)
            steps = 2000
            repex.simulate(steps)
            self.assertTrue(exchanged)
            expected = 0.5*integrator.getTemperature()*MOLAR_GAS_CONSTANT_R
            for i in range(len(r2)):
                average = 0.5*states[i]['k']*r2[i]/steps
                self.assertTrue(0.7 < average/expected < 1.3)