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.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', comm_server=('two.radical-project.org', 33243))
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 step 1:
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 # pdb.set_trace()