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():
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',
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)
s0.system = system
s0.cutoff = 12.0
s0.switchdist = 10.0
s0.pairlistdist = 13.5
s0.numsteps = 1000
# append step 0 to protocol:
p0.append(s0)
# 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"
# set all values that have <placeholder> in the *.conf file
# import pdb