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Using the faster LangevinDynamicsMove #1138

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Jan 10, 2023
Merged

Using the faster LangevinDynamicsMove #1138

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c3ed493
Using the faster LangevinDynamicsMove
ijpulidos Jan 6, 2023
deeadd7
Removing splitting kwarg.
ijpulidos Jan 6, 2023
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2 changes: 1 addition & 1 deletion perses/app/setup_relative_calculation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -706,7 +706,7 @@ def run_setup(setup_options, serialize_systems=True, build_samplers=True):
hss[phase].energy_context_cache = energy_context_cache
hss[phase].sampler_context_cache = sampler_context_cache
elif setup_options['fe_type'] == 'repex':
hss[phase] = HybridRepexSampler(mcmc_moves=mcmc.LangevinSplittingDynamicsMove(
hss[phase] = HybridRepexSampler(mcmc_moves=mcmc.LangevinDynamicsMove(
timestep=timestep,
collision_rate=1.0 / unit.picosecond,
n_steps=n_steps_per_move_application,
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4 changes: 2 additions & 2 deletions perses/tests/test_repex.py
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Expand Up @@ -54,7 +54,7 @@ def test_RESTCapableHybridTopologyFactory_repex_neutral_mutation():
# Set up repex simulation
reporter_file = os.path.join(temp_dir, f"{wt_name}-{mutant_name}.nc")
reporter = MultiStateReporter(reporter_file, checkpoint_interval=10)
hss = HybridRepexSampler(mcmc_moves=mcmc.LangevinSplittingDynamicsMove(timestep=4.0 * unit.femtoseconds,
hss = HybridRepexSampler(mcmc_moves=mcmc.LangevinDynamicsMove(timestep=4.0 * unit.femtoseconds,
collision_rate=1.0 / unit.picosecond,
n_steps=50,
reassign_velocities=False,
Expand Down Expand Up @@ -157,7 +157,7 @@ def test_RESTCapableHybridTopologyFactory_repex_charge_mutation():
# Set up repex simulation
reporter_file = os.path.join(temp_dir, f"{wt_name}-{mutant_name}.nc")
reporter = MultiStateReporter(reporter_file, checkpoint_interval=10)
hss = HybridRepexSampler(mcmc_moves=mcmc.LangevinSplittingDynamicsMove(timestep=4.0 * unit.femtoseconds,
hss = HybridRepexSampler(mcmc_moves=mcmc.LangevinDynamicsMove(timestep=4.0 * unit.femtoseconds,
collision_rate=1.0 / unit.picosecond,
n_steps=50,
reassign_velocities=False,
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9 changes: 3 additions & 6 deletions perses/tests/test_resume.py
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Expand Up @@ -127,13 +127,12 @@ def test_resume_small_molecule():
checkpoint_interval=checkpoint_interval,
)
hss = HybridRepexSampler(
mcmc_moves=mcmc.LangevinSplittingDynamicsMove(
mcmc_moves=mcmc.LangevinDynamicsMove(
timestep=4.0 * unit.femtoseconds,
collision_rate=5.0 / unit.picosecond,
n_steps=250,
reassign_velocities=False,
n_restart_attempts=20,
splitting="V R R R O R R R V",
constraint_tolerance=1e-06,
),
hybrid_factory=htf,
Expand Down Expand Up @@ -197,13 +196,12 @@ def test_resume_protein_mutation_with_checkpoint(tmp_path):
checkpoint_interval=checkpoint_interval,
)
hss = HybridRepexSampler(
mcmc_moves=mcmc.LangevinSplittingDynamicsMove(
mcmc_moves=mcmc.LangevinDynamicsMove(
timestep=4.0 * unit.femtoseconds,
collision_rate=5.0 / unit.picosecond,
n_steps=250,
reassign_velocities=False,
n_restart_attempts=20,
splitting="V R R R O R R R V",
constraint_tolerance=1e-06,
),
hybrid_factory=htf,
Expand Down Expand Up @@ -268,13 +266,12 @@ def test_resume_protein_mutation_no_checkpoint(tmp_path):
checkpoint_interval=checkpoint_interval,
)
hss = HybridRepexSampler(
mcmc_moves=mcmc.LangevinSplittingDynamicsMove(
mcmc_moves=mcmc.LangevinDynamicsMove(
timestep=4.0 * unit.femtoseconds,
collision_rate=5.0 / unit.picosecond,
n_steps=250,
reassign_velocities=False,
n_restart_attempts=20,
splitting="V R R R O R R R V",
constraint_tolerance=1e-06,
),
hybrid_factory=htf,
Expand Down
4 changes: 2 additions & 2 deletions perses/tests/testsystems.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
import numpy as np
from functools import partial
from openmmtools import states
from openmmtools.mcmc import MCMCSampler, LangevinSplittingDynamicsMove
from openmmtools.mcmc import MCMCSampler, LangevinDynamicsMove
from perses.utils.smallmolecules import sanitizeSMILES, canonicalize_SMILES
from perses.storage import NetCDFStorage, NetCDFStorageView
from perses.rjmc.topology_proposal import OESMILES_OPTIONS
Expand Down Expand Up @@ -117,7 +117,7 @@ def __init__(self, storage_filename=None, mode='w', ncmc_nsteps=5, mcmc_nsteps=1
self._timestep = 1.0*unit.femtosecond
self._ncmc_nsteps = ncmc_nsteps
self._mcmc_nsteps = mcmc_nsteps
self._move = LangevinSplittingDynamicsMove(timestep=self._timestep, splitting=self._splitting, n_restart_attempts=10)
self._move = LangevinDynamicsMove(timestep=self._timestep, splitting=self._splitting, n_restart_attempts=10)
self._move.n_restart_attempts = 10


Expand Down