def ufed_model(
temp=300 * unit.kelvin,
mass=50 * unit.dalton * (unit.nanometer / unit.radians)**2,
Ks=1000 * unit.kilojoules_per_mole / unit.radians**2,
Ts=1500 * unit.kelvin,
limit=180 * unit.degrees,
sigma=18 * unit.degrees,
height=0.0,
frequency=10,
enforce_gridless=False,
):
model = ufedmm.AlanineDipeptideModel()
s_phi = ufedmm.DynamicalVariable('s_phi',
-limit,
limit,
mass,
Ts,
model.phi,
Ks,
sigma=sigma)
s_psi = ufedmm.DynamicalVariable('s_psi',
-limit,
limit,
mass,
Ts,
model.psi,
Ks,
sigma=sigma)
return model, ufedmm.UnifiedFreeEnergyDynamics(
[s_phi, s_psi],
temp,
height,
frequency,
enforce_gridless=enforce_gridless)
def test_radius_of_gyration():
model = ufedmm.AlanineDipeptideModel()
R = model.positions._value
N = len(R)
Rmean = sum(R, openmm.Vec3(0, 0, 0)) / N
RgSqVal = 0.0
for r in R:
dr = r - Rmean
RgSqVal += dr.x**2 + dr.y**2 + dr.z**2
RgSqVal /= N
RgSq = cvlib.SquareRadiusOfGyration(range(model.topology._numAtoms))
RgSq.setForceGroup(1)
model.system.addForce(RgSq)
Rg = cvlib.RadiusOfGyration(range(model.topology._numAtoms))
Rg.setForceGroup(2)
model.system.addForce(Rg)
integrator = openmm.CustomIntegrator(0)
platform = openmm.Platform.getPlatformByName('Reference')
context = openmm.Context(model.system, integrator, platform)
context.setPositions(model.positions)
RgSq = context.getState(getEnergy=True,
groups={1}).getPotentialEnergy()._value
assert RgSq == pytest.approx(RgSqVal)
Rg = context.getState(getEnergy=True,
groups={2}).getPotentialEnergy()._value
assert Rg * Rg == pytest.approx(RgSqVal)
def test_inner_exceptions():
model = ufedmm.AlanineDipeptideModel()
nbforce = next(
filter(lambda f: isinstance(f, openmm.NonbondedForce),
model.system.getForces()))
rs = 0.2
rc = 0.4
ufedmm.add_inner_nonbonded_force(model.system, rs, rc, 1)
model.system.getForce(model.system.getNumForces() - 1).setForceGroup(3)
platform = openmm.Platform.getPlatformByName('Reference')
context = openmm.Context(model.system, openmm.CustomIntegrator(0),
platform)
context.setPositions(model.positions)
forces1 = _standardized(
context.getState(getForces=True, groups={3}).getForces())
forces2 = [0 * f for f in forces1]
ONE_4PI_EPS0 = 138.93545764438198
for index in range(nbforce.getNumExceptions()):
i, j, chargeprod, sigma, epsilon = map(
_standardized, nbforce.getExceptionParameters(index))
rij = _standardized(model.positions[i] - model.positions[j])
r = np.linalg.norm(rij)
z = (r - rs) / (rc - rs)
F = S(z) * (24 * epsilon * (2 * (sigma / r)**12 - (sigma / r)**6) / r +
ONE_4PI_EPS0 * chargeprod / r**2) * rij / r
forces2[i] += F
forces2[j] -= F
for f1, f2 in zip(forces1, forces2):
for i in range(3):
assert f1[i] == pytest.approx(f2[i])
def ufed_model():
model = ufedmm.AlanineDipeptideModel()
mass = 50*unit.dalton*(unit.nanometer/unit.radians)**2
Ks = 1000*unit.kilojoules_per_mole/unit.radians**2
Ts = 1500*unit.kelvin
limit = 180*unit.degrees
sigma = 18*unit.degrees
height = 2.0*unit.kilojoules_per_mole
frequency = 10
phi = ufedmm.CollectiveVariable('phi', model.phi, -limit, limit, mass, Ks, Ts, sigma)
psi = ufedmm.CollectiveVariable('psi', model.psi, -limit, limit, mass, Ks, Ts, sigma)
return model, ufedmm.UnifiedFreeEnergyDynamics([phi, psi], 300*unit.kelvin, height, frequency)
def test_in_out_lennard_jones_force():
model = ufedmm.AlanineDipeptideModel(water='tip3p')
before = potential_energy(model.system, model.positions,
openmm.NonbondedForce)
solute_atoms = [
atom.index for atom in model.topology.atoms()
if atom.residue.name != 'HOH'
]
nbforce = next(
filter(lambda f: isinstance(f, openmm.NonbondedForce),
model.system.getForces()))
in_out_LJ = cvlib.InOutLennardJonesForce(solute_atoms, nbforce)
model.system.addForce(in_out_LJ)
after = potential_energy(
model.system, model.positions,
(openmm.NonbondedForce, openmm.CustomNonbondedForce))
assert after / after.unit == pytest.approx(before / before.unit, 1E-2)
choices=waters,
default=None)
parser.add_argument('--ff',
dest='ff',
help='the pepdide force field',
default='amber03')
parser.add_argument('--seed', dest='seed', help='the RNG seed', default=None)
parser.add_argument('--platform',
dest='platform',
help='the computation platform',
default='Reference')
args = parser.parse_args()
seed = random.SystemRandom().randint(0, 2**
31) if args.seed is None else args.seed
model = ufedmm.AlanineDipeptideModel(force_field=args.ff, water=args.water)
temp = 300 * unit.kelvin
gamma = 10 / unit.picoseconds
dt = 2 * unit.femtoseconds
nsteps = 1000000
mass = 30 * unit.dalton * (unit.nanometer / unit.radians)**2
Ks = 1000 * unit.kilojoules_per_mole / unit.radians**2
Ts = 1500 * unit.kelvin
limit = 180 * unit.degrees
sigma = 18 * unit.degrees
height = 2.0 * unit.kilojoules_per_mole
deposition_period = 200
phi = ufedmm.CollectiveVariable('phi', model.phi, -limit, limit, mass, Ks, Ts,
sigma)
psi = ufedmm.CollectiveVariable('psi', model.psi, -limit, limit, mass, Ks, Ts,
sigma)