From c3ed4937c3d0f909f4c024fd82a69ba5ac16981d Mon Sep 17 00:00:00 2001 From: ijpulidos <2949729+ijpulidos@users.noreply.github.com> Date: Thu, 5 Jan 2023 23:20:15 -0500 Subject: [PATCH 1/2] Using the faster LangevinDynamicsMove --- perses/app/setup_relative_calculation.py | 2 +- perses/tests/test_repex.py | 4 ++-- perses/tests/test_resume.py | 6 +++--- perses/tests/testsystems.py | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/perses/app/setup_relative_calculation.py b/perses/app/setup_relative_calculation.py index b5c87eab3..2a362ac28 100644 --- a/perses/app/setup_relative_calculation.py +++ b/perses/app/setup_relative_calculation.py @@ -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, diff --git a/perses/tests/test_repex.py b/perses/tests/test_repex.py index 9b1466f51..a4c235a2e 100644 --- a/perses/tests/test_repex.py +++ b/perses/tests/test_repex.py @@ -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, @@ -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, diff --git a/perses/tests/test_resume.py b/perses/tests/test_resume.py index 354b59e31..3ecfd3528 100644 --- a/perses/tests/test_resume.py +++ b/perses/tests/test_resume.py @@ -127,7 +127,7 @@ 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, @@ -197,7 +197,7 @@ 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, @@ -268,7 +268,7 @@ 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, diff --git a/perses/tests/testsystems.py b/perses/tests/testsystems.py index 6c521c919..0873d3c97 100644 --- a/perses/tests/testsystems.py +++ b/perses/tests/testsystems.py @@ -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 @@ -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 From deeadd7c49d9d07b6e2bd97f4271754761481498 Mon Sep 17 00:00:00 2001 From: ijpulidos <2949729+ijpulidos@users.noreply.github.com> Date: Fri, 6 Jan 2023 00:04:28 -0500 Subject: [PATCH 2/2] Removing splitting kwarg. --- perses/tests/test_resume.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/perses/tests/test_resume.py b/perses/tests/test_resume.py index 3ecfd3528..2c2f42a76 100644 --- a/perses/tests/test_resume.py +++ b/perses/tests/test_resume.py @@ -133,7 +133,6 @@ def test_resume_small_molecule(): 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, @@ -203,7 +202,6 @@ def test_resume_protein_mutation_with_checkpoint(tmp_path): 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, @@ -274,7 +272,6 @@ def test_resume_protein_mutation_no_checkpoint(tmp_path): 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,