sams_sampler.verbose = True
# DEBUG: Write PDB of initial frame
print("Writing initial frame to 'initial.pdb'...")
from simtk.openmm.app import PDBFile
outfile = open('initial.pdb', 'w')
PDBFile.writeFile(topology, positions, outfile)
outfile.close()
# Run the simulation
print('Running simulation...')
#exen_sampler.update_scheme = 'restricted-range' # scheme for deciding which alchemical state to jump to
exen_sampler.update_scheme = 'global-jump' # scheme for deciding which alchemical state to jump to
#exen_sampler.locality = thermodynamic_state_neighbors # neighbors to examine for each state
sams_sampler.update_method = 'rao-blackwellized' # scheme for updating free energy estimates
niterations = 20000 # number of iterations to run
sams_sampler.run(niterations) # run sampler
ncfile.close()
# Analyze
from sams import analysis
# States
from collections import namedtuple
MockTestsystem = namedtuple('MockTestsystem', ['description', 'thermodynamic_states'])
testsystem = MockTestsystem(description='DDR1 umbrella states', thermodynamic_states=thermodynamic_states)
analysis.analyze(netcdf_filename, testsystem, 'output.pdf')
# Write trajectory
reference_pdb_filename = 'trajectory.pdb'
trajectory_filename = 'trajectory.xtc'
analysis.write_trajectory(netcdf_filename, topology, reference_pdb_filename, trajectory_filename)
sams_sampler.verbose = True
# DEBUG: Write PDB of initial frame
print("Writing initial frame to 'initial.pdb'...")
from simtk.openmm.app import PDBFile
outfile = open('initial.pdb', 'w')
PDBFile.writeFile(topology, positions, outfile)
outfile.close()
# Run the simulation
print('Running simulation...')
#exen_sampler.update_scheme = 'restricted-range' # scheme for deciding which alchemical state to jump to
exen_sampler.update_scheme = 'global-jump' # scheme for deciding which alchemical state to jump to
#exen_sampler.locality = thermodynamic_state_neighbors # neighbors to examine for each state
sams_sampler.update_method = 'rao-blackwellized' # scheme for updating free energy estimates
niterations = 20000 # number of iterations to run
sams_sampler.run(niterations) # run sampler
ncfile.close()
# Analyze
from sams import analysis
# States
from collections import namedtuple
MockTestsystem = namedtuple('MockTestsystem', ['description', 'thermodynamic_states'])
testsystem = MockTestsystem(description='DDR1 umbrella states', thermodynamic_states=thermodynamic_states)
analysis.analyze(netcdf_filename, testsystem, 'output.pdf')
# Write trajectory
reference_pdb_filename = 'trajectory.pdb'
trajectory_filename = 'trajectory.xtc'
analysis.write_trajectory(netcdf_filename, topology, reference_pdb_filename, trajectory_filename)
# Create thermodynamic states
thermodynamic_states = list()
# Umbrella off state
parameters = {
'umbrella1_K' : 0.0, 'umbrella1_r0' : 0.0, # umbrella parameters
'umbrella2_K' : 0.0, 'umbrella2_r0' : 0.0, # umbrella parameters
}
thermodynamic_states.append( ThermodynamicState(system=system, temperature=temperature, pressure=pressure, parameters=parameters) )
# Umbrella on state
alchemical_lambda = 0.0
for umbrella1_distance in umbrella_distances:
for umbrella2_distance in umbrella_distances:
parameters = {
'umbrella1_K' : umbrella_K.value_in_unit_system(unit.md_unit_system), 'umbrella1_r0' : umbrella1_distance.value_in_unit_system(unit.md_unit_system), # umbrella parameters
'umbrella2_K' : umbrella_K.value_in_unit_system(unit.md_unit_system), 'umbrella2_r0' : umbrella2_distance.value_in_unit_system(unit.md_unit_system), # umbrella parameters
}
thermodynamic_states.append( ThermodynamicState(system=system, temperature=temperature, pressure=pressure, parameters=parameters) )
# Analyze
from sams import analysis
# States
from collections import namedtuple
MockTestsystem = namedtuple('MockTestsystem', ['description', 'thermodynamic_states'])
testsystem = MockTestsystem(description='DDR1 umbrella states', thermodynamic_states=thermodynamic_states)
analysis.analyze(netcdf_filename, testsystem, '2d-distance-output.pdf')
# Write trajectory
analysis.write_trajectory(netcdf_filename, topology, pdb_trajectory_filename, xtc_trajectory_filename)
#pdb_filename = resource_filename('sams', os.path.join('data', 'abl-imatinib', 'inhibitor.pdb'))
#generate_ffxml(pdb_filename)
#stop
netcdf_filename = 'output2.nc'
#testsystem = HarmonicOscillatorSimulatedTempering(netcdf_filename=netcdf_filename)
#testsystem = AblImatinibVacuumAlchemical(netcdf_filename=netcdf_filename)
testsystem = AblImatinibExplicitAlchemical(netcdf_filename=netcdf_filename)
#testsystem = HostGuestAlchemical(netcdf_filename=netcdf_filename)
#testsystem = AlanineDipeptideExplicitAlchemical()
#testsystem = AlanineDipeptideVacuumSimulatedTempering(netcdf_filename=netcdf_filename)
#testsystem = AlanineDipeptideExplicitSimulatedTempering(netcdf_filename=netcdf_filename)
#testsystem = WaterBoxAlchemical(netcdf_filename=netcdf_filename)
testsystem.exen_sampler.update_scheme = 'restricted-range'
testsystem.mcmc_sampler.nsteps = 2500
testsystem.exen_sampler.locality = 5
testsystem.sams_sampler.update_method = 'rao-blackwellized'
niterations = 5000
#testsystem.sams_sampler.run(niterations)
# Test analysis
from sams.analysis import analyze, write_trajectory
netcdf_filename = 'output.nc'
analyze(netcdf_filename, testsystem, 'analyze.pdf')
reference_pdb_filename = 'output.pdb'
dcd_trajectory_filename = 'output.dcd'
trajectory_filename = 'output.xtc'
write_trajectory(netcdf_filename, testsystem.topology, reference_pdb_filename, trajectory_filename)
parameters = {
'umbrella1_K':
umbrella_K.value_in_unit_system(unit.md_unit_system),
'umbrella1_r0':
umbrella1_distance.value_in_unit_system(
unit.md_unit_system), # umbrella parameters
'umbrella2_K':
umbrella_K.value_in_unit_system(unit.md_unit_system),
'umbrella2_r0':
umbrella2_distance.value_in_unit_system(
unit.md_unit_system), # umbrella parameters
}
thermodynamic_states.append(
ThermodynamicState(system=system,
temperature=temperature,
pressure=pressure,
parameters=parameters))
# Analyze
from sams import analysis
# States
from collections import namedtuple
MockTestsystem = namedtuple('MockTestsystem',
['description', 'thermodynamic_states'])
testsystem = MockTestsystem(description='DDR1 umbrella states',
thermodynamic_states=thermodynamic_states)
analysis.analyze(netcdf_filename, testsystem, '2d-distance-output.pdf')
# Write trajectory
analysis.write_trajectory(netcdf_filename, topology, pdb_trajectory_filename,
xtc_trajectory_filename)
#generate_ffxml(pdb_filename)
#stop
netcdf_filename = 'output2.nc'
#testsystem = HarmonicOscillatorSimulatedTempering(netcdf_filename=netcdf_filename)
#testsystem = AblImatinibVacuumAlchemical(netcdf_filename=netcdf_filename)
testsystem = AblImatinibExplicitAlchemical(netcdf_filename=netcdf_filename)
#testsystem = HostGuestAlchemical(netcdf_filename=netcdf_filename)
#testsystem = AlanineDipeptideExplicitAlchemical()
#testsystem = AlanineDipeptideVacuumSimulatedTempering(netcdf_filename=netcdf_filename)
#testsystem = AlanineDipeptideExplicitSimulatedTempering(netcdf_filename=netcdf_filename)
#testsystem = WaterBoxAlchemical(netcdf_filename=netcdf_filename)
testsystem.exen_sampler.update_scheme = 'restricted-range'
testsystem.mcmc_sampler.nsteps = 2500
testsystem.exen_sampler.locality = 5
testsystem.sams_sampler.update_method = 'rao-blackwellized'
niterations = 5000
#testsystem.sams_sampler.run(niterations)
# Test analysis
from sams.analysis import analyze, write_trajectory
netcdf_filename = 'output.nc'
analyze(netcdf_filename, testsystem, 'analyze.pdf')
reference_pdb_filename = 'output.pdb'
dcd_trajectory_filename = 'output.dcd'
trajectory_filename = 'output.xtc'
write_trajectory(netcdf_filename, testsystem.topology,
reference_pdb_filename, trajectory_filename)
