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 __init__(self,
force_field='amber03',
water=None,
box_length=25 * unit.angstroms,
constraints=openmm.app.HBonds,
rigidWater=True):
pdb = app.PDBFile(
os.path.join(ufedmm.__path__[0], 'data', 'alanine-dipeptide.pdb'))
if water is None:
force_field = app.ForceField(f'{force_field}.xml')
self.topology = pdb.topology
self.positions = pdb.positions
L = box_length.value_in_unit(unit.nanometers)
vectors = [
openmm.Vec3(L, 0, 0),
openmm.Vec3(0, L, 0),
openmm.Vec3(0, 0, L)
]
self.topology.setPeriodicBoxVectors(vectors)
else:
force_field = app.ForceField(f'{force_field}.xml', f'{water}.xml')
modeller = app.Modeller(pdb.topology, pdb.positions)
modeller.addSolvent(force_field,
model=water,
boxSize=box_length * openmm.Vec3(1, 1, 1))
self.topology = modeller.topology
self.positions = modeller.positions
self.system = force_field.createSystem(
self.topology,
nonbondedMethod=app.NoCutoff if water is None else app.PME,
constraints=constraints,
rigidWater=rigidWater,
removeCMMotion=False,
)
atoms = [(a.name, a.residue.name) for a in self.topology.atoms()]
phi_atoms = [('C', 'ACE'), ('N', 'ALA'), ('CA', 'ALA'), ('C', 'ALA')]
self.phi = ufedmm.CollectiveVariable(
'phi', openmm.CustomTorsionForce('theta'))
self.phi.force.addTorsion(*[atoms.index(i) for i in phi_atoms], [])
psi_atoms = [('N', 'ALA'), ('CA', 'ALA'), ('C', 'ALA'), ('N', 'NME')]
self.psi = ufedmm.CollectiveVariable(
'psi', openmm.CustomTorsionForce('theta'))
self.psi.force.addTorsion(*[atoms.index(i) for i in psi_atoms], [])
def dihedral_angle_cvs(prmtop_file, name, *atom_types):
selected_dihedrals = set()
for dihedral in pmd.amber.AmberParm(prmtop_file).dihedrals:
atoms = [getattr(dihedral, f'atom{i+1}') for i in range(4)]
if all(a.type == atype for a, atype in zip(atoms, atom_types)):
selected_dihedrals.add(tuple(a.idx for a in atoms))
n = len(selected_dihedrals)
collective_variables = []
for i, dihedral in enumerate(selected_dihedrals):
force = openmm.CustomTorsionForce('theta')
force.addTorsion(*dihedral, [])
cv_name = name if n == 1 else f'{name}{i+1}'
cv = ufedmm.CollectiveVariable(cv_name, force)
collective_variables.append(cv)
# print(cv_name, dihedral)
return collective_variables
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)
ufed = ufedmm.UnifiedFreeEnergyDynamics([phi, psi], temp, height,
deposition_period)
ufedmm.serialize(ufed, 'ufed_object.yml')
integrator = ufedmm.GeodesicBAOABIntegrator(temp, gamma, dt)
integrator.setRandomNumberSeed(seed)
platform = openmm.Platform.getPlatformByName(args.platform)
simulation = ufed.simulation(model.topology, model.system, integrator,
platform)
ufed.set_positions(simulation, model.positions)
ufed.set_random_velocities(simulation, seed)
output = ufedmm.MultipleFiles(stdout, 'output.csv')
reporter = ufedmm.StateDataReporter(output,
100,
Ts = 3000 * unit.kelvin
sigma = 0.05
height = 2.0 * unit.kilojoules_per_mole
deposition_period = 200
pdb = app.PDBFile('aaqaa3.pdb')
force_field = app.ForceField('charmm36.xml')
system = force_field.createSystem(
pdb.topology,
nonbondedMethod=app.NoCutoff,
constraints=None,
rigidWater=False,
removeCMMotion=False,
)
hc_hb = ufedmm.CollectiveVariable(
'hc_hb', cvlib.HelixHydrogenBondContent(pdb.topology, 0, 14))
hc_a = ufedmm.CollectiveVariable('hc_a',
cvlib.HelixAngleContent(pdb.topology, 0, 14))
hc_d = ufedmm.CollectiveVariable(
'hc_d', cvlib.HelixRamachandranContent(pdb.topology, 0, 14))
s_hc = ufedmm.DynamicalVariable('s_hc',
0.0,
1.0,
mass,
Ts, [hc_hb, hc_a, hc_d],
'0.5*Ks*(s_hc - (hc_hb + hc_a + hc_d)/3)^2',
Ks=Ks,
sigma=sigma,
periodic=False)