def _dihedralTerm(self, n, phase, V):
mod_file = self.mod_template % \
(V/(Units.kcal/Units.mol), phase/Units.deg, n)
ff = Amber99ForceField(mod_files=[StringIO(mod_file)])
self.universe.setForceField(ff)
param = self.universe.energyEvaluatorParameters()
i1, i2, i3, i4, n_test, phase_test, V_test = \
param['cosine_dihedral_term'][0]
self.assertEqual(n_test, n)
# The accuracy is no better than five digits because the
# parameters pass through a text representation.
self.assertAlmostEqual(phase_test, phase, 5)
self.assertAlmostEqual(V_test, V, 5)
two_pi = 2. * N.pi
m = self.universe[0]
for angle in N.arange(0., two_pi, 0.1):
m.C4.setPosition(Vector(N.cos(angle), N.sin(angle), 1.))
e = self.universe.energyTerms()['cosine dihedral angle']
da = self.universe.dihedral(m.C1, m.C2, m.C3, m.C4)
e_ref = V * (1. + N.cos(n * angle - phase))
self.assertAlmostEqual(angle % two_pi, da % two_pi, 14)
self.assertAlmostEqual(e, e_ref, 5)
self._gradientTest()
self._forceConstantTest()
def setUp(self):
self.universe = MMTK.InfiniteUniverse(Amber99ForceField())
self.universe.peptide = Protein('bala1')
self.subspace = RigidMotionSubspace(self.universe,
self.universe.peptide.residues())
def setUp(self):
self.universe = MMTK.InfiniteUniverse(Amber99ForceField())
self.universe.water = MMTK.Molecule('water')
velocities += dv
configuration += delta_t*velocities
universe.setConfiguration(configuration)
energy, gradients = evaluator(gradients)
dv = -0.5*delta_t*gradients*inv_masses
velocities += dv
universe.setVelocities(velocities)
time += delta_t
snapshot(data={'time': time,
'potential_energy': energy})
if equilibration_temperature is not None \
and step % equilibration_frequency == 0:
universe.scaleVelocitiesToTemperature(equilibration_temperature)
# Define system
universe = InfiniteUniverse(Amber99ForceField())
universe.protein = Protein('bala1')
# Create trajectory and snapshot generator
trajectory = Trajectory(universe, "md_trajectory.nc", "w",
"Generated by a Python integrator")
snapshot = SnapshotGenerator(universe,
actions = [TrajectoryOutput(trajectory,
["all"], 0, None, 1)])
# Initialize velocities
universe.initializeVelocitiesToTemperature(50.*Units.K)
# Heat and equilibrate
for temperature in [50., 100., 200., 300.]:
doVelocityVerletSteps(delta_t = 1.*Units.fs, nsteps = 500,
equilibration_temperature = temperature*Units.K,
elem = bsubstr(line, 32, 2)
if elem[1] == ' ':
elem = elem[0]
name.append(elem + str(atmi))
factory.addAtom('main', name[atmi - 1], elem)
factory.setPosition('main',name[atmi-1],Vector\
(x*Units.Ang, y*Units.Ang, z*Units.Ang))
if linecnt >= (5 + natm):
if line[0] == 'M': break
factory.addBond('main',\
name[int(bsubstr(line,1,3))-1], name[int(bsubstr(line,4,3))-1])
fpo1.close()
newmol = factory.retrieveMolecule('main')
universe = InfiniteUniverse(Amber99ForceField(mod_files=['frcmod.ff99SB']))
universe.addObject(newmol)
universe.configuration()
# -------------------------------------------
#anchor(universe) # BUG pseudo01.sdf when first atom has only one bond
#universe.writeXML(file('out.xml', 'w'));
#universe.writeToFile('out.pdb');
convertor = bConvertor(universe)
convertor.cart2all_internals()
#convertor.print_internals()
#print '\n++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n'
def setUp(self):
self.universe = MMTK.InfiniteUniverse(Amber99ForceField())
self.universe.water1 = MMTK.Molecule('water',
position=MMTK.Vector(0., 0., 0.))
self.universe.water2 = MMTK.Molecule('water',
position=MMTK.Vector(0.5, 0., 0.))
def setUp(self):
self.universe = MMTK.InfiniteUniverse(Amber99ForceField())
self.universe.peptide = Protein('bala1')