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 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 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 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)
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)
s0.system = system
s0.cutoff = 12.0
s0.switchdist = 10.0
s0.pairlistdist = 13.5
from htbac import Protocol, Runner, Simulation, System, AbFile
from htbac.protocols import Esmacs
# Load systems
systems = list()
# Create protocol
esm = Protocol(clone_settings=False)
# Create simulations and add them to the protocol
for step, numsteps in zip(Esmacs.steps, Esmacs.numsteps):
sim = Simulation()
sim.engine = 'namd_openmp_cuda'
sim.cutoff = 10.0
sim.switchingdist = 8.0
sim.pairlistdist = 11.5
sim.water_model = 'tip4'
# This is present in step 3 only.
sim.numsmallsteps = 20000
sim.numsteps = numsteps
sim.add_input_file(step, is_executable_argument=True)
sim.add_ensemble('replica', range(25))
sim.add_ensemble('system', systems)
# 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
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"
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:
p = 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, 0.95, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.05,
0.00
])
s0.add_input_file("default_configs/rfe/54353507-54150798/eq0.conf",
is_executable_argument=True)
s0.system = system