Exemplos de ReplicaExchange.resume_repex em Python

Exemplo n.º 1

Arquivo: test_mpi.py Projeto: andrrizzi/repex

pdb_filename = "./1vii.pdb"

temperature = 300 * u.kelvin
friction = 0.3 / u.picosecond
timestep = 2.0 * u.femtosecond

forcefield = app.ForceField("amber10.xml", "tip3p.xml")

pdb = app.PDBFile(pdb_filename)

model = app.modeller.Modeller(pdb.topology, pdb.positions)
model.addSolvent(forcefield, padding=0.01 * u.nanometer)

system = forcefield.createSystem(
    model.topology, nonbondedMethod=app.PME, nonbondedCutoff=1.0 * u.nanometers, constraints=app.HAngles
)

states = [ThermodynamicState(system=system, temperature=T_i[i]) for i in range(n_replicas)]

coordinates = [model.getPositions()] * n_replicas

# database = repex.netcdf_io.NetCDFDatabase(nc_filename, states, coordinates)

# replica_exchange = ReplicaExchange(states, coordinates, nc_filename)
# replica_exchange = ReplicaExchange.create_repex(states, coordinates, nc_filename,  mpicomm=MPI.COMM_WORLD, **{})
replica_exchange = ReplicaExchange.resume_repex(nc_filename, mpicomm=MPI.COMM_WORLD, **{})
replica_exchange.number_of_iterations = 30
replica_exchange.run()

Exemplo n.º 2

T_i = [ T_min + (T_max - T_min) * (np.exp(float(i) / float(n_replicas-1)) - 1.0) / (np.e - 1.0) for i in range(n_replicas) ]


pdb_filename = "./1vii.pdb"

temperature = 300 * u.kelvin
friction = 0.3 / u.picosecond
timestep = 2.0 * u.femtosecond

forcefield = app.ForceField("amber10.xml", "tip3p.xml")

pdb = app.PDBFile(pdb_filename)

model = app.modeller.Modeller(pdb.topology, pdb.positions)
model.addSolvent(forcefield, padding=0.01 * u.nanometer)

system = forcefield.createSystem(model.topology, nonbondedMethod=app.PME, nonbondedCutoff=1.0 * u.nanometers, constraints=app.HAngles)

states = [ ThermodynamicState(system=system, temperature=T_i[i]) for i in range(n_replicas) ]

coordinates = [model.getPositions()] * n_replicas

#database = repex.netcdf_io.NetCDFDatabase(nc_filename, states, coordinates)

#replica_exchange = ReplicaExchange(states, coordinates, nc_filename)
#replica_exchange = ReplicaExchange.create_repex(states, coordinates, nc_filename,  mpicomm=MPI.COMM_WORLD, **{})
replica_exchange = ReplicaExchange.resume_repex(nc_filename, mpicomm=MPI.COMM_WORLD, **{})
replica_exchange.number_of_iterations = 30
replica_exchange.run()

Exemplo n.º 3

Arquivo: test_serial.py Projeto: zhenglz/repex

temperature = 300 * u.kelvin
friction = 0.3 / u.picosecond
timestep = 2.0 * u.femtosecond

forcefield = app.ForceField("amber10.xml", "tip3p.xml")

pdb = app.PDBFile(pdb_filename)

model = app.modeller.Modeller(pdb.topology, pdb.positions)
model.addSolvent(forcefield, padding=0.01 * u.nanometer)

system = forcefield.createSystem(model.topology,
                                 nonbondedMethod=app.PME,
                                 nonbondedCutoff=1.0 * u.nanometers,
                                 constraints=app.HAngles)

states = [
    ThermodynamicState(system=system, temperature=T_i[i])
    for i in range(n_replicas)
]

coordinates = [model.getPositions()] * n_replicas

#database = repex.netcdf_io.NetCDFDatabase(nc_filename, states, coordinates)

#replica_exchange = ReplicaExchange(states, coordinates, nc_filename)
#replica_exchange = ReplicaExchange.create_repex(states, coordinates, nc_filename, **{})
replica_exchange = ReplicaExchange.resume_repex(nc_filename, **{})
replica_exchange.number_of_iterations = 20
replica_exchange.run()

Exemplo n.º 4

Arquivo: test_serial.py Projeto: andrrizzi/repex

T_i = [ T_min + (T_max - T_min) * (np.exp(float(i) / float(n_replicas-1)) - 1.0) / (np.e - 1.0) for i in range(n_replicas) ]


pdb_filename = "./1vii.pdb"

temperature = 300 * u.kelvin
friction = 0.3 / u.picosecond
timestep = 2.0 * u.femtosecond

forcefield = app.ForceField("amber10.xml", "tip3p.xml")

pdb = app.PDBFile(pdb_filename)

model = app.modeller.Modeller(pdb.topology, pdb.positions)
model.addSolvent(forcefield, padding=0.01 * u.nanometer)

system = forcefield.createSystem(model.topology, nonbondedMethod=app.PME, nonbondedCutoff=1.0 * u.nanometers, constraints=app.HAngles)

states = [ ThermodynamicState(system=system, temperature=T_i[i]) for i in range(n_replicas) ]

coordinates = [model.getPositions()] * n_replicas

#database = repex.netcdf_io.NetCDFDatabase(nc_filename, states, coordinates)

#replica_exchange = ReplicaExchange(states, coordinates, nc_filename)
#replica_exchange = ReplicaExchange.create_repex(states, coordinates, nc_filename, **{})
replica_exchange = ReplicaExchange.resume_repex(nc_filename, **{})
replica_exchange.number_of_iterations = 20
replica_exchange.run()