def construct_simulator(name,
top,
sys,
pos,
timestep=default_timestep,
thinning_interval=default_thinning):
return EquilibriumSimulator(platform=configure_platform("CUDA"),
topology=top,
system=sys,
positions=pos,
temperature=temperature,
timestep=timestep,
burn_in_length=burn_in_length,
n_samples=n_samples,
thinning_interval=thinning_interval,
name=name)
from benchmark.testsystems.configuration import configure_platform
import numpy as np
n_samples = 100
thinning_interval = 100
temperature = simulation_parameters["temperature"]
from benchmark.testsystems.bookkeepers import EquilibriumSimulator
top, sys, pos = load_alanine(constrained=True)
alanine_constrained = EquilibriumSimulator(
platform=configure_platform("Reference"),
topology=top,
system=sys,
positions=pos,
temperature=temperature,
timestep=1.0 * unit.femtosecond,
burn_in_length=500,
n_samples=n_samples,
thinning_interval=thinning_interval,
name="alanine_constrained_test")
print("Sample from cache: \n", alanine_constrained.sample_x_from_equilibrium())
sim = NonequilibriumSimulator(
alanine_constrained,
LangevinSplittingIntegrator("O V R V O", timestep=4.5 * unit.femtoseconds))
result = sim.collect_protocol_samples(100,
100,
store_potential_energy_traces=True,
store_W_shad_traces=True)
print("<W>_(0 -> M): {:.3f}, <W>_(M -> 2M): {:.3f}".format(
testsystem = WaterBox(constrained=constrained)
(topology, system,
positions) = testsystem.topology, testsystem.system, testsystem.positions
add_barostat(system)
return topology, system, positions
temperature = simulation_parameters["temperature"]
from benchmark.testsystems.bookkeepers import EquilibriumSimulator
top, sys, pos = load_waterbox(constrained=True)
waterbox_constrained = EquilibriumSimulator(
platform=configure_platform("CUDA"),
topology=top,
system=sys,
positions=pos,
temperature=temperature,
timestep=1.0 * unit.femtosecond,
burn_in_length=100000,
n_samples=1000,
thinning_interval=10000,
name="waterbox_constrained")
top, sys, pos = load_waterbox(constrained=False)
flexible_waterbox = EquilibriumSimulator(platform=configure_platform("CUDA"),
topology=top,
system=sys,
positions=pos,
temperature=temperature,
timestep=0.5 * unit.femtosecond,
burn_in_length=200000,
n_samples=1000,
force.addBond(int(bond[0]), int(bond[1]), grid_spacing, coupling_strength)
system.addForce(force)
# Create topology.
topology = app.Topology()
element = app.Element.getBySymbol('Ar')
chain = topology.addChain()
for particle in range(system.getNumParticles()):
residue = topology.addResidue('Ar', chain)
topology.addAtom('Ar', element, residue)
# Set topology, positions, system as instance attributes
self.topology = topology
self.positions = positions
self.system = system
n_samples = 1000 # number of samples to collect
if 'TRAVIS' in os.environ:
n_samples = 20 # reduce sampling for travis
temperature = simulation_parameters["temperature"]
testsystem = CoupledPowerOscillators(nx=5, ny=5, nz=5)
top, sys, pos = testsystem.topology, testsystem.system, testsystem.positions
coupled_power_oscillators = EquilibriumSimulator(platform=configure_platform("CPU"),
topology=top, system=sys, positions=pos,
temperature=temperature,
timestep=1.0 * unit.femtosecond,
burn_in_length=1000, n_samples=n_samples,
thinning_interval=10, name="coupled_power_oscillators")
else:
testsystem = AlanineDipeptideExplicit(constraints=None, rigid_water=False)
topology, system, positions = testsystem.topology, testsystem.system, testsystem.positions
add_barostat(system)
return topology, system, positions
n_samples = 1000 # number of samples to collect
if 'TRAVIS' in os.environ:
n_samples = 20 # reduce sampling for travis
temperature = simulation_parameters["temperature"]
from benchmark.testsystems.bookkeepers import EquilibriumSimulator
top, sys, pos = load_alanine(constrained=True)
alanine_constrained = EquilibriumSimulator(platform=configure_platform("Reference"),
topology=top, system=sys, positions=pos,
temperature=temperature,
timestep=1.0 * unit.femtosecond,
burn_in_length=50000, n_samples=n_samples,
thinning_interval=10000, name="alanine_constrained")
top, sys, pos = load_alanine(constrained=False)
alanine_unconstrained = EquilibriumSimulator(platform=configure_platform("Reference"),
topology=top, system=sys, positions=pos,
temperature=temperature,
timestep=1.0 * unit.femtosecond,
burn_in_length=50000, n_samples=n_samples,
thinning_interval=10000, name="alanine_unconstrained")
top, sys, pos = load_solvated_alanine(constrained=False)
solvated_alanine_unconstrained = EquilibriumSimulator(platform=configure_platform("CUDA"),
topology=top, system=sys, positions=pos,
temperature=temperature,
# DHFR reaction field (for the MTS experiment)
dhfr_reaction_field = construct_simulator(
"dhfr_constrained_reaction_field",
*load_dhfr_reaction_field(constrained=True))
# Src explicit
top, sys, pos = load_src_explicit(constrained=True)
src_constrained = construct_simulator("src_constrained", top, sys, pos,
default_timestep / 2.5,
default_thinning * 2.5)
# T4 lysozyme
t4_constrained = construct_simulator("t4_constrained",
*load_t4_implicit(constrained=True))
t4_unconstrained = construct_simulator("t4_unconstrained",
*load_t4_implicit(constrained=False))
# constraint-coupled harmonic oscillators
top, sys, pos = load_constraint_coupled_harmonic_oscillators(constrained=True)
constraint_coupled_harmonic_oscillators = EquilibriumSimulator(
platform=configure_platform("Reference"),
topology=top,
system=sys,
positions=pos,
temperature=temperature,
timestep=1000.0 * unit.femtosecond,
burn_in_length=50,
n_samples=10000,
thinning_interval=10,
name="constraint_coupled_harmonic_oscillators")
self.system = system
self.positions = positions
n_waters = 20
testsystem = WaterCluster(n_waters=n_waters, constrained=True)
(topology, system,
positions) = testsystem.topology, testsystem.system, testsystem.positions
water_cluster_rigid = EquilibriumSimulator(
platform=configure_platform("Reference"),
topology=topology,
system=system,
positions=positions,
temperature=temperature,
timestep=1.0 * unit.femtosecond,
burn_in_length=100000,
n_samples=1000,
thinning_interval=10000,
name="water_cluster_rigid")
testsystem = WaterCluster(n_waters=n_waters, constrained=False)
(topology, system,
positions) = testsystem.topology, testsystem.system, testsystem.positions
water_cluster_flexible = EquilibriumSimulator(
platform=configure_platform("Reference"),
topology=topology,
system=system,
positions=positions,