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()
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()
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()
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()