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[WIP] SAMS samplers and documentation #214

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[WIP] SAMS samplers and documentation #214

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df02715
Initial import of SAMS samplers and documentation
jchodera Jun 5, 2017
7fba8d3
Fix typo in netcdf4 conda package requirements
jchodera Jun 5, 2017
f0ee1e6
Add analysis module temporarily
jchodera Jun 5, 2017
e366db5
Rework MCMCSampler usage to match openmmtools.mcmc
jchodera Jun 5, 2017
10e2eca
Don't make a deep copy of ThermodynamicState when constructing MCMCSa…
jchodera Jun 5, 2017
070a894
Comment out timing and ncfile use until interface is replaced
jchodera Jun 5, 2017
5df3dd5
Draft storage and timing infrastructure.
jchodera Jun 9, 2017
f691f53
Update docs
jchodera Jul 7, 2017
f77417b
Merge remote-tracking branch 'origin/master' into sams
jchodera Aug 2, 2017
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Rework MCMCSampler usage to match openmmtools.mcmc
@jchodera
jchodera committed Jun 5, 2017
commit e366db535438f93aa0d5004c9016e1a076618ab2
1 change: 0 additions & 1 deletion openmmtools/mcmc.py
View file
Original file line number Diff line number Diff line change
@@ -291,7 +291,6 @@ def minimize(self, tolerance=1.0*unit.kilocalories_per_mole/unit.angstroms,

timer.report_timing()


# =============================================================================
# MCMC MOVE CONTAINERS
# =============================================================================
59 changes: 22 additions & 37 deletions openmmtools/samplers/sams/testsystems.py
View file
Original file line number Diff line number Diff line change
@@ -31,7 +31,7 @@
from openmmtools import testsystems
from openmmtools.states import ThermodynamicState, SamplerState
from openmmtools.mcmc import MCMCSampler, GHMCMove, LangevinDynamicsMove
from openmmtools.samplers.sams import ExpandedEnsembleSampler, SAMSSampler
from openmmtools.samplers.sams import ExpandedEnsemble, SAMS

################################################################################
# CONSTANTS
@@ -97,10 +97,10 @@ class SAMSTestSystem(object):
Themodynamic states for each environment
mcmc_samplers : dict of MCMCSampler objects
MCMCSampler objects for environments
exen_samplers : dict of ExpandedEnsembleSampler objects
ExpandedEnsembleSampler objects for environments
sams_samplers : dict of SAMSSampler objects
SAMSSampler objects for environments
exen_samplers : dict of ExpandedEnsemble objects
ExpandedEnsemble objects for environments
sams_samplers : dict of SAMS objects
SAMS objects for environments

"""
def __init__(self, netcdf_filename=None):
@@ -141,6 +141,7 @@ def __init__(self, **kwargs):
mass = 39.948 * unit.amu # 3D harmonic oscillator particle mass
period = 2.0 * np.pi * unit.sqrt(mass / K) # harmonic oscillator period
timestep = 0.01 * period
collision_rate = 1.0 / (100 * timestep)
testsystem = HarmonicOscillator(K=K, mass=mass)
self.topology = testsystem.topology
self.positions = testsystem.positions
@@ -164,16 +165,11 @@ def __init__(self, **kwargs):
thermodynamic_state_index = 0 # initial thermodynamic state index
thermodynamic_state = self.thermodynamic_states[thermodynamic_state_index]
sampler_state = SamplerState(positions=self.positions)
self.mcmc_sampler = MCMCSampler(sampler_state=sampler_state, thermodynamic_state=thermodynamic_state, ncfile=self.ncfile)
self.mcmc_sampler.pdbfile = open('output.pdb', 'w')
self.mcmc_sampler.topology = self.topology
self.mcmc_sampler.timestep = timestep
self.mcmc_sampler.collision_rate = 1.0 / (100 * timestep)
self.mcmc_sampler.nsteps = 1000
self.mcmc_sampler.verbose = True
self.exen_sampler = ExpandedEnsembleSampler(self.mcmc_sampler, self.thermodynamic_states)
mcmc_move = LangevinDynamicsMove(timestep=timestep, collision_rate=collision_rate, n_steps=1000)
self.mcmc_sampler = MCMCSampler(thermodynamic_state, sampler_state, move=mcmc_move)
self.exen_sampler = ExpandedEnsemble(self.mcmc_sampler, self.thermodynamic_states)
self.exen_sampler.verbose = True
self.sams_sampler = SAMSSampler(self.exen_sampler, update_stages='two-stage', update_method='optimal')
self.sams_sampler = SAMS(self.exen_sampler, update_stages='two-stage', update_method='optimal')
self.sams_sampler.verbose = True


@@ -221,14 +217,11 @@ def __init__(self, **kwargs):
thermodynamic_state_index = 0 # initial thermodynamic state index
thermodynamic_state = self.thermodynamic_states[thermodynamic_state_index]
sampler_state = SamplerState(positions=self.positions)
self.mcmc_sampler = MCMCSampler(sampler_state=sampler_state, thermodynamic_state=thermodynamic_state, ncfile=self.ncfile)
self.mcmc_sampler.pdbfile = open('output.pdb', 'w')
self.mcmc_sampler.topology = self.topology
self.mcmc_sampler.nsteps = 500 # reduce number of steps for testing
self.mcmc_sampler.verbose = True
self.exen_sampler = ExpandedEnsembleSampler(self.mcmc_sampler, self.thermodynamic_states)
mcmc_move = LangevinDynamicsMove(n_steps=500)
self.mcmc_sampler = MCMCSampler(thermodynamic_state, sampler_state, mcmc_move)
self.exen_sampler = ExpandedEnsemble(self.mcmc_sampler, self.thermodynamic_states)
self.exen_sampler.verbose = True
self.sams_sampler = SAMSSampler(self.exen_sampler)
self.sams_sampler = SAMS(self.exen_sampler)
self.sams_sampler.verbose = True

class AlanineDipeptideExplicitSimulatedTempering(SAMSTestSystem):
@@ -287,15 +280,11 @@ def __init__(self, **kwargs):
thermodynamic_state_index = 0 # initial thermodynamic state index
thermodynamic_state = self.thermodynamic_states[thermodynamic_state_index]
sampler_state = SamplerState(positions=self.positions)
self.mcmc_sampler = MCMCSampler(sampler_state=sampler_state, thermodynamic_state=thermodynamic_state, ncfile=self.ncfile)
#self.mcmc_sampler.pdbfile = open('output.pdb', 'w')
self.mcmc_sampler.topology = self.topology
self.mcmc_sampler.nsteps = 500
self.mcmc_sampler.timestep = 2.0 * unit.femtoseconds
self.mcmc_sampler.verbose = True
self.exen_sampler = ExpandedEnsembleSampler(self.mcmc_sampler, self.thermodynamic_states)
mcmc_move = LangevinDynamicsMove(timestep=2.0*unit.femtoseconds, n_steps=500)
self.mcmc_sampler = MCMCSampler(thermodynamic_state, sampler_state=sampler_state)
self.exen_sampler = ExpandedEnsemble(self.mcmc_sampler, self.thermodynamic_states)
self.exen_sampler.verbose = True
self.sams_sampler = SAMSSampler(self.exen_sampler)
self.sams_sampler = SAMS(self.exen_sampler)
self.sams_sampler.verbose = True

class AlchemicalSAMSTestSystem(SAMSTestSystem):
@@ -386,15 +375,11 @@ def __init__(self, alchemical_protocol='two-phase', nlambda=50, **kwargs):
thermodynamic_state_index = 0 # initial thermodynamic state index
thermodynamic_state = self.thermodynamic_states[thermodynamic_state_index]
sampler_state = SamplerState(positions=self.positions)
self.mcmc_sampler = MCMCSampler(sampler_state=sampler_state, thermodynamic_state=thermodynamic_state, ncfile=self.ncfile)
self.mcmc_sampler.timestep = 2.0 * unit.femtoseconds
self.mcmc_sampler.nsteps = 500
#self.mcmc_sampler.pdbfile = open('output.pdb', 'w')
self.mcmc_sampler.topology = self.topology
self.mcmc_sampler.verbose = True
self.exen_sampler = ExpandedEnsembleSampler(self.mcmc_sampler, self.thermodynamic_states)
mcmc_move = LangevinDynamicsMove(timestep=2.0*unit.femtoseconds, n_steps=500)
self.mcmc_sampler = MCMCSampler(thermodynamic_state, sampler_state=sampler_state)
self.exen_sampler = ExpandedEnsemble(self.mcmc_sampler, self.thermodynamic_states)
self.exen_sampler.verbose = True
self.sams_sampler = SAMSSampler(self.exen_sampler)
self.sams_sampler = SAMS(self.exen_sampler)
self.sams_sampler.verbose = True

# DEBUG: Write PDB of initial frame