def run_afe():
system = System(prefix='systems/dov-wt')
afe = Simulation()
afe.system = system
afe.engine = 'namd'
afe.cores = 2
afe.numminsteps = 10
afe.numsteps = 10
afe.add_input_file(Afe.step0, is_executable_argument=True)
afe.add_input_file('inputs/restraint.in', is_executable_argument=False)
afe.add_ensemble('replica', range(2))
afe.add_ensemble('lambdawindow', [0.0, 1.0])
afe.cutoff = 12.0
afe.switchdist = 10.0
afe.pairlistdist = 13.5
afe.k1 = 10
afe.k2 = 500
ht = Runner(comm_server=('two.radical-project.org', 33146))
ht.add_protocol(afe)
ht.run(walltime=1000)
def run_rfe():
pdb = AbFile('systems/ptp1b-l1-l2-complex.pdb', tag='pdb')
top = AbFile('systems/ptp1b-l1-l2-complex.top', tag='topology')
tag = AbFile('systems/ptp1b-l1-l2-tags.pdb', tag='alchemicaltags')
cor = AbFile('systems/ptp1b-l1-l2-complex.inpcrd', tag='coordinate')
system = System(name='ptp1b-l1-l2', files=[pdb, top, tag, cor])
p = Protocol(clone_settings=False)
for step, numsteps in zip(Rfe.steps, [5000, 50000]):
rfe = Simulation()
rfe.system = system
rfe.engine = 'namd_mpi'
rfe.cores = 32
rfe.cutoff = 12.0
rfe.switchdist = 10.0
rfe.pairlistdist = 13.5
rfe.numminsteps = 5000
rfe.numsteps = numsteps
rfe.add_input_file(step, is_executable_argument=True)
rfe.add_ensemble('replica', range(1))
# to increase the number of EnTK tasks: change the lambdawindow parameter
rfe.add_ensemble('lambdawindow', [1.])
p.append(rfe)
ht = Runner('bw_aprun', comm_server=('two.radical-project.org', 33158))
ht.add_protocol(p)
ht.run(walltime=480, queue='high')
def test_simulation_component():
s0 = Simulation(name='minimizer')
s0.engine = 'titan_orte'
s0.processes = 1
s0.threads_per_process = 16
s0.add_ensemble('replica', range(5))
pdb = AbFile('systems/ptp1b-l1-l2-complex.pdb', tag='pdb')
top = AbFile('systems/ptp1b-l1-l2-complex.top', tag='topology')
tag = AbFile('systems/ptp1b-l1-l2-tags.pdb', tag='alchemicaltags')
cor = AbFile('systems/ptp1b-l1-l2-complex.inpcrd', tag='coordinate')
system = System(name='ptp1b-l1-l2', files=[pdb, top, tag, cor])
s0.system = system
assert s0.name == 'minimizer'
assert s0.engine == 'titan_orte'
assert s0.system.name == 'ptp1b-l1-l2'
assert s0._processes == 1
assert s0._threads_per_process == 16
len_ensemble = reduce(mul, (len(v) for v in s0._ensembles.itervalues()), 1)
assert s0.cpus == s0.threads_per_process * s0._processes * len_ensemble
assert s0.shared_data == [
'systems/ptp1b-l1-l2-complex.pdb', 'systems/ptp1b-l1-l2-complex.top',
'systems/ptp1b-l1-l2-tags.pdb', 'systems/ptp1b-l1-l2-complex.inpcrd'
]
s1 = Simulation(name='equilibrate')
def run_rfe(s, steps, proc):
pdb = AbFile('{}.pdb'.format(s), tag='pdb')
top = AbFile('{}.prmtop'.format(s), tag='topology')
tag = AbFile('{}_tags.pdb'.format(s), tag='alchemicaltags')
cor = AbFile('{}.inpcrd'.format(s), tag='coordinate')
system = System(name='1z3f-intercalator-complex',
files=[pdb, top, tag, cor])
p = Protocol(RFE.minimize(), RFE.simulation(), RFE.simulation(),
RFE.simulation(), RFE.simulation(), RFE.simulation(),
RFE.simulation(), DataAggregate(extension=".alch"))
step_counts = [1000, 500, 500, 1000, 1000, 10000, steps]
for rfe, numsteps in zip(p.simulations(), step_counts):
rfe.system = system
rfe.engine = 'namd'
rfe.processes = proc
rfe.threads_per_process = 1
rfe.cutoff = 10.0
rfe.switchdist = 8.0
rfe.pairlistdist = 11.5
rfe.numsteps = numsteps
rfe.watermodel = 'tip3'
rfe.add_ensemble('replica', range(5))
rfe.add_ensemble('lambdawindow', [
0.0, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 1.0
])
ht = Runner('bw_aprun', comm_server=('two.radical-project.org', 33227))
ht.add_protocol(p)
ht.run(walltime=1440, queue='high')
def run_rfe():
pdb = AbFile('systems/ptp1b-l1-l2-complex.pdb', tag='pdb')
top = AbFile('systems/ptp1b-l1-l2-complex.top', tag='topology')
tag = AbFile('systems/ptp1b-l1-l2-tags.pdb', tag='alchemicaltags')
cor = AbFile('systems/ptp1b-l1-l2-complex.inpcrd', tag='coordinate')
system = System(name='ptp1b-l1-l2', files=[pdb, top, tag, cor])
p = RFE()
p.append(DataAggregate(extension=".alch"))
# Protocol `p` is made up of 3 steps:
# minimize -> simulate -> aggregate data
for sim, numsteps in zip(p.simulations(), [5000, 2000000]):
sim.system = system
sim.engine = 'namd'
sim.processes = 32
sim.threads_per_process = 1
sim.cutoff = 12.0
sim.switchdist = 10.0
sim.pairlistdist = 13.5
sim.watermodel = "tip3"
sim.numsteps = numsteps
sim.add_ensemble('replica', range(5))
sim.add_ensemble('lambdawindow', [1.0, 0.95, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4,
0.3, 0.2, 0.1, 0.05, 0.0])
ht = Runner('bw_aprun', comm_server=('two.radical-project.org', 33048))
ht.add_protocol(p)
ht.run(walltime=720, queue='low')
def test_replica_systems_simulation():
s1 = System(prefix='nilotinib-e255k')
s2 = System(prefix='nilotinib-e255v')
sim = EnsembleSimulation()
sim.config = 'simple.conf'
sim.engine = engine
sim.add_ensemble('system', [s1, s2])
sim.add_ensemble('replica', range(2))
ht = Runner(resource=resource)
ht.rabbitmq_config(**rabbit_mq)
ht.add_protocol(sim)
ht.run(**run_conf)
def test_protocol():
s1 = System(prefix='nilotinib-e255k')
s2 = System(prefix='nilotinib-e255v')
sim1 = EnsembleSimulation()
sim1.config = 'protocol_1.conf'
sim1.engine = engine
sim1.cores = 2
sim1.add_ensemble('system', [s1, s2])
sim1.add_ensemble('replica', range(2))
sim1.add_placeholder('numsteps', 10)
sim1.add_placeholder('cutoff', 10.0)
sim1.add_placeholder('switchingdist', 8.0)
sim1.add_placeholder('pairlistdist', 11.5)
sim1.add_placeholder('water_model', 'tip4')
sim2 = EnsembleSimulation()
sim2.config = 'protocol_2.conf'
sim2.engine = engine
sim2.cores = 2
sim2.add_placeholder('numsteps', 10)
sim2.add_placeholder('cutoff', 10.0)
sim2.add_placeholder('switchingdist', 8.0)
sim2.add_placeholder('pairlistdist', 11.5)
sim2.add_placeholder('water_model', 'tip4')
p = Protocol()
p.add_simulation(sim1)
p.add_simulation(sim2)
ht = Runner(resource=resource)
ht.rabbitmq_config(**rabbit_mq)
ht.add_protocol(p)
ht.run(**run_conf)
def test_single_simulation():
system = System(prefix='nilotinib-e255k')
sim = BaseSimulation()
sim.system = system
sim.config = 'simple.conf'
sim.engine = engine
ht = Runner(resource=resource)
ht.rabbitmq_config(**rabbit_mq)
ht.add_protocol(sim)
ht.run(**run_conf)
def test_configurable_simulation():
s1 = System(prefix='nilotinib-e255k')
sim = BaseSimulation()
sim.system = s1
sim.config = 'configurable.conf'
sim.engine = engine
sim.add_placeholder('numsteps', 1000)
sim.add_placeholder('cutoff', 10.0)
sim.add_placeholder('switchingdist', 8.0)
sim.add_placeholder('pairlistdist', 11.5)
sim.add_placeholder('water_model', 'tip4')
ht = Runner(resource=resource)
ht.rabbitmq_config(**rabbit_mq)
ht.add_protocol(sim)
ht.run(**run_conf)
def run_rfe():
pdb = AbFile('complex.pdb', tag='pdb')
top = AbFile('complex.prmtop', tag='topology')
tag = AbFile('tags.pdb', tag='alchemicaltags')
cor = AbFile('complex.inpcrd', tag='coordinate')
system = System(name='1z3f-l08-l11', files=[pdb, top, tag, cor])
p = Protocol(clone_settings=False)
min, run = Rfe.steps
for step, numsteps in zip([min, run, run, run, run, run],
[100, 500, 1000, 1000, 1000, 10000, 8000000]):
rfe = Simulation()
rfe.system = system
rfe.engine = 'namd'
rfe.processes = 8
rfe.threads_per_process = 16
rfe.cutoff = 10.0
rfe.switchdist = 8.0
rfe.pairlistdist = 11.5
rfe.numsteps = numsteps
rfe.watermodel = 'tip4'
rfe.add_input_file(step, is_executable_argument=True)
rfe.add_ensemble('replica', range(3))
# to increase the number of EnTK tasks: change the lambdawindow parameter
rfe.add_ensemble('lambdawindow', np.linspace(0, 1, 13))
p.append(rfe)
ht = Runner('titan_aprun')
ht.add_protocol(p)
ht.run(walltime=720)
from htbac import Runner, Protocol, Simulation, System, AbFile
from htbac.analysis import GradientBoostClassifier
# Step 0: load system files.
coord = AbFile('systems/nilotinib-e255k-complex.inpcrd', tag='coordinate')
top = AbFile('systems/nilotinib-e255k-complex.top', tag='topology')
system = System(name='nilotinib-e255k', files=[top, coord])
# Step 1: create a Simulation
sim = Simulation()
sim.engine = 'openmm'
sim.system = system
sim.processes = 1
sim.threads_per_process = 32
sim.numsteps = 1000
sim.add_input_file('inputs/benchmark.py', is_executable_argument=True)
# Step 2: Hyperparameter optimization using HyperSpace Gradient Boost Classifier
# analysis = GradientBoostClassifier()
# analysis.hyperparameters = 4
# analysis.data_path = '/pylon5/mc3bggp/dakka/hyperspace_data/constellation/constellation/data/fashion'
# analysis.optimization_file = '/home/jdakka/hyperspace/constellation/constellation/gbm/space4/optimize.py'
# analysis.results_dir = '/pylon5/mc3bggp/dakka/hyperspace_data/results_space_4'
ht = Runner('xsede.bridges_gpu',
from htbac import Runner, Protocol, Simulation, System, AbFile, DataAggregate, TiesAnalysis, AdaptiveQuadrature
# define system
pdb = AbFile('systems/54353507-54150798/54353507-54150798-complex.pdb',
tag='pdb')
top = AbFile('systems/54353507-54150798/54353507-54150798-complex.top',
tag='topology')
tag = AbFile('systems/54353507-54150798/54353507-54150798-tags.pdb',
tag='alchemicaltags')
cor = AbFile('systems/54353507-54150798/54353507-54150798-complex.crd',
tag='coordinate')
cons = AbFile('systems/54353507-54150798/54353507-54150798-cons.pdb',
tag='constraint')
fep = AbFile('systems/54353507-54150798/54353507-54150798-fep.tcl',
tag='source')
system = System(name='54353507-54150798',
files=[pdb, top, tag, cor, cons, fep])
# Create simulation steps for relative free energy protocol
# define protocol:
p0 = Protocol()
# define step 0:
s0 = Simulation(name='minimizer')
s0.engine = 'namd'
s0.processes = 32
s0.threads_per_process = 1
s0.add_ensemble('replica', range(5))
s0.add_ensemble('lambdawindow', [1.00, 0.50, 0.00])
s0.add_input_file("default_configs/rfe/54353507-54150798/eq0.conf",
is_executable_argument=True)
# Import HTBAC modules from htbac import Protocol, Simulation, System # Import built in simulation protocol configurations # like relative free energy calculations, or esmacs from htbac.protocols import Rfe, Afe, Esmacs # Step 0: load system files. system = System(prefix='systems/ptp1b-l1-l2') # Step 1: create the container protocol p = Protocol() # Step 2: create a simulation that minimizes and equilibrate the system s0 = Simulation(name='minimizer') s0.system = system
name = "{}-{}".format(s, r)
folder = "{}/{}-{}/build/".format(prefix, s, r)
rest_folder = "{}/{}-{}/restraints/".format(prefix, s, r)
pdb = AbFile(folder + "complex.pdb", tag='pdb').with_prefix(name)
top = AbFile(folder + "complex.prmtop",
tag='topology').with_prefix(name)
coord = AbFile(folder + "complex.rst7",
tag='coordinate').with_prefix(name)
rest = AbFile(rest_folder + "restraint_1.0.in",
tag='restraint',
needs_copying=True).with_prefix(name)
tags = AbFile(folder + "tags.pdb",
tag='alchemicaltags').with_prefix(name).with_prefix(name)
systems.append(System(name, files=[pdb, top, coord, rest, tags]))
sim = Simulation()
sim.engine = 'dummy' # This *forces* the core count to 1, non mpi.
sim.cutoff = 12.0
sim.pairlistdist = 13.5
sim.switchdist = 10.0
sim.numsteps = Afe.numsteps[0]
sim.add_ensemble('replica', values=range(5))
sim.add_ensemble('system', values=systems)
sim.add_ensemble(
'lambdawindow',
values=[0.0, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0])
from htbac import Runner, Protocol, Simulation, System, AbFile, DataAggregate
from htbac.protocols import RFE, ESMACS # Allows users to utilize pre-defined protocols
# define system
pdb = AbFile('systems/ptp1b-l1-l2-complex.pdb', tag='pdb')
top = AbFile('systems/ptp1b-l1-l2-complex.top', tag='topology')
tag = AbFile('systems/ptp1b-l1-l2-tags.pdb', tag='alchemicaltags')
cor = AbFile('systems/ptp1b-l1-l2-complex.inpcrd', tag='coordinate')
system = System(name='ptp1b-l1-l2', files=[pdb, top, tag, cor])
# Create simulation steps for relative free energy protocol
# define protocol:
p = Protocol()
# define step 0:
s0 = Simulation(name='minimizer')
s0.engine = 'namd'
s0.processes = 1
s0.threads_per_process = 16
s0.add_ensemble('replica', range(5))
s0.add_ensemble('lambdawindow', [1.0, 0.5, 0.0])
s0.add_input_file("default_configs/rfe/ties-0.conf",
is_executable_argument=True)
s0.system = system
s0.cutoff = 12.0
s0.switchdist = 10.0
s0.pairlistdist = 13.5
s0.numsteps = 5000
s0.watermodel = "tip3"
from htbac import Runner, Protocol, Simulation, System, AbFile, DataAggregate
# define system
pdb = AbFile('systems/esmacs-pde2-4d08-l1/esmacs-pde2-4d08-l1-complex.pdb',
tag='pdb')
top = AbFile('systems/esmacs-pde2-4d08-l1/esmacs-pde2-4d08-l1-complex.top',
tag='topology')
cons = AbFile('systems/esmacs-pde2-4d08-l1/esmacs-pde2-4d08-l1-f4.pdb',
tag='constraint')
cor = AbFile('systems/esmacs-pde2-4d08-l1/esmacs-pde2-4d08-l1-complex.crd',
tag='coordinate')
fep = AbFile('systems/esmacs-pde2-4d08-l1/esmacs-pde2-4d08-l1-fep.tcl',
tag='source')
system = System(name='esmacs-pde2-4d08-l1', files=[pdb, top, cons, cor, fep])
# Create simulation steps for relative free energy protocol
# define protocol:
p = Protocol()
# define step 0:
s0 = Simulation(name='stage-0')
s0.engine = 'namd'
s0.processes = 32
s0.threads_per_process = 1
s0.add_ensemble('replica', range(25))
s0.add_input_file(
"default_configs/esmacs/esmacs-pde2-4d08-l1/esmacs-stage-0.conf",
is_executable_argument=True)
s0.system = system