def test_reporters_pbc(self):
""" Test NetCDF and ASCII restart and trajectory reporters (w/ PBC) """
systemsolv = load_file(self.get_fn('ildn.solv.top'),
xyz=self.get_fn('ildn.solv.gro'))
system = systemsolv.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8 * u.angstroms)
integrator = mm.LangevinIntegrator(300 * u.kelvin, 5.0 / u.picoseconds,
1.0 * u.femtoseconds)
sim = app.Simulation(systemsolv.topology, system, integrator, CPU)
sim.context.setPositions(systemsolv.positions)
sim.reporters.extend([
NetCDFReporter(self.get_fn('traj.nc', written=True),
1,
vels=True,
frcs=True),
MdcrdReporter(self.get_fn('traj.mdcrd', written=True), 1),
RestartReporter(self.get_fn('restart.ncrst', written=True),
1,
netcdf=True),
RestartReporter(self.get_fn('restart.rst7', written=True), 1),
StateDataReporter(self.get_fn('state.o', written=True),
1,
volume=True,
density=True,
systemMass=1)
])
sim.step(5)
for reporter in sim.reporters:
reporter.finalize()
ntraj = NetCDFTraj.open_old(self.get_fn('traj.nc', written=True))
atraj = AmberMdcrd(self.get_fn('traj.mdcrd', written=True),
len(systemsolv.atoms),
True,
mode='r')
nrst = NetCDFRestart.open_old(
self.get_fn('restart.ncrst', written=True))
arst = AmberAsciiRestart(self.get_fn('restart.rst7', written=True),
'r')
self.assertEqual(ntraj.frame, 5)
self.assertEqual(atraj.frame, 5)
self.assertTrue(ntraj.hasvels)
self.assertTrue(ntraj.hasfrcs)
for i in range(ntraj.frame):
for x1, x2 in zip(ntraj.box[i], atraj.box[i]):
self.assertAlmostEqual(x1, x2, places=3)
self.assertEqual(len(nrst.box), 6)
self.assertEqual(len(arst.box), 6)
# Make sure the EnergyMinimizerReporter does not fail
f = StringIO()
rep = EnergyMinimizerReporter(f, volume=True)
rep.report(sim)
rep.finalize()
def test_state_data_reporter(self):
""" Test StateDataReporter with various options """
system = self.amber_gas.createSystem()
integrator = mm.LangevinIntegrator(300 * u.kelvin, 5.0 / u.picoseconds,
1.0 * u.femtoseconds)
sim = app.Simulation(self.amber_gas.topology,
system,
integrator,
platform=CPU)
sim.context.setPositions(self.amber_gas.positions)
f = open(self.get_fn('akma5.dat', written=True), 'w')
sim.reporters.extend([
StateDataReporter(self.get_fn('akma1.dat', written=True), 10),
StateDataReporter(self.get_fn('akma2.dat', written=True),
10,
time=False,
potentialEnergy=False,
kineticEnergy=False,
totalEnergy=False,
temperature=False),
StateDataReporter(self.get_fn('akma3.dat', written=True),
10,
volume=True,
density=True),
StateDataReporter(self.get_fn('akma4.dat', written=True),
10,
separator='\t'),
StateDataReporter(self.get_fn('units.dat', written=True),
10,
volume=True,
density=True,
energyUnit=u.kilojoules_per_mole,
volumeUnit=u.nanometers**3),
StateDataReporter(f, 10)
])
sim.step(500)
f.close()
# Now open all of the reporters and check that the information in there
# is what we expect it to be
akma1 = open(self.get_fn('akma1.dat', written=True), 'r')
akma2 = open(self.get_fn('akma2.dat', written=True), 'r')
akma3 = open(self.get_fn('akma3.dat', written=True), 'r')
akma4 = open(self.get_fn('akma4.dat', written=True), 'r')
akma5 = open(self.get_fn('akma5.dat', written=True), 'r')
units = open(self.get_fn('units.dat', written=True), 'r')
# AKMA 1 first
header = akma1.readline().strip()[1:].split(',')
self.assertEqual(len(header), 6)
for i, label in enumerate(
('Step', 'Time', 'Potential Energy', 'Kinetic Energy',
'Total Energy', 'Temperature')):
self.assertTrue(label in header[i])
for i, line in enumerate(akma1):
words = line.replace('\n', '').split(',')
self.assertEqual(i * 10 + 10, int(words[0])) # step
akma1.close()
# AKMA 2
header = akma2.readline().strip()[1:].split(',')
self.assertEqual(len(header), 1)
self.assertTrue('Step' in header[0])
for i, line in enumerate(akma2):
self.assertEqual(int(line.replace('\n', '').split(',')[0]),
10 * i + 10)
akma2.close()
# AKMA 3 -- save energies so we can compare to the file with different
# units
header = akma3.readline().strip()[1:].split(',')
self.assertEqual(len(header), 8)
for i, label in enumerate(
('Step', 'Time', 'Potential Energy', 'Kinetic Energy',
'Total Energy', 'Temperature', 'Box Volume', 'Density')):
self.assertTrue(label in header[i])
akma_energies = [[0.0 for i in range(8)] for j in range(50)]
for i, line in enumerate(akma3):
words = line.replace('\n', '').split(',')
akma_energies[i][0] = int(words[0])
for j in range(1, 8):
akma_energies[i][j] = float(words[j])
akma3.close()
# AKMA 4 -- tab delimiter
header = akma4.readline().strip()[1:].split('\t')
self.assertEqual(len(header), 6)
for i, label in enumerate(
('Step', 'Time', 'Potential Energy', 'Kinetic Energy',
'Total Energy', 'Temperature')):
self.assertTrue(label in header[i])
for i, line in enumerate(akma4):
words = line.replace('\n', '').split('\t')
self.assertEqual(i * 10 + 10, int(words[0])) # step
akma4.close()
# AKMA 5 -- write to open file handle
header = akma5.readline().strip()[1:].split(',')
self.assertEqual(len(header), 6)
for i, label in enumerate(
('Step', 'Time', 'Potential Energy', 'Kinetic Energy',
'Total Energy', 'Temperature')):
self.assertTrue(label in header[i])
for i, line in enumerate(akma5):
words = line.replace('\n', '').split(',')
self.assertEqual(i * 10 + 10, int(words[0])) # step
akma5.close()
# UNITS -- compare other units
ene = u.kilojoule_per_mole.conversion_factor_to(u.kilocalorie_per_mole)
volume = u.nanometers.conversion_factor_to(u.angstroms)**3
conversions = [1, 1, ene, ene, ene, 1, volume, 1]
headers = units.readline().strip()[1:].split(',')
self.assertEqual(len(headers), 8)
for i, line in enumerate(units):
words = line.replace('\n', '').split(',')
self.assertEqual(int(words[0]), akma_energies[i][0])
for j in range(1, 8):
self.assertAlmostEqual(float(words[j]) * conversions[j],
akma_energies[i][j],
places=5)
units.close()
# Change to CUDA platform
platform = mm.openmm.Platform.getPlatformByName('CUDA')
properties = {'CudaDeviceIndex': '1'} # you can add other things like the precision here
# Create our Simulation object with our system and chosen integrator
sim = app.Simulation(om_solv.topology, system, integrator, platform, properties)
# Set the positions from our PDB file
sim.context.setPositions(om_crds.positions)
# Minimize Energy
print("Minimizing Energy")
sim.minimizeEnergy()
# Reporters
print("Appending Reporters")
sim.reporters.append(StateDataReporter(sys.stdout, round(steps/10), step=True,
potentialEnergy=False, kineticEnergy=False,
temperature=True, volume=True, density=False))
# Write out to DCD file
sim.reporters.append(app.DCDReporter('tryps_ben_solv.dcd', report_steps))
# Run (100ns)
sim.step(steps)