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])
sim.add_input_file(Afe.step0, is_executable_argument=True)
sim.add_variable(name='k1', value=10, in_file='*restraint_1.0.in')
sim.add_variable(name='k2', value=500, in_file='*restraint_1.0.in')
runner = Runner(resource='local',
comm_server=('two.radical-project.org', 33166))
runner.add_protocol(sim)
# Customize resource to the type of python installed locally.
runner.run(resource='local.localhost_anaconda', walltime=10000)
sim = Simulation()
sim.engine = 'namd_mpi'
sim.cores = 32
sim.cutoff = 12.0
sim.pairlistdist = 13.5
sim.switchdist = 10.0
sim.numsteps = numsteps
sim.add_ensemble('replica', values=range(2))
sim.add_ensemble('system', values=systems[:2])
sim.add_ensemble('lambdawindow',
values=[
1.0, 0.75, 0.5, 0.3, 0.2, 0.15, 0.1, 0.075, 0.05, 0.025,
0.01, 0.0
][:2])
sim.add_input_file(step, is_executable_argument=True)
sim.add_variable(name='k1',
value=property(lambda: 10 * sim.lambdawindow),
in_file='*restraint_1.0.in')
sim.add_variable(name='k2',
value=property(lambda: 500 * sim.lambdawindow),
in_file='*restraint_1.0.in')
runner = Runner(resource='bw_aprun',
comm_server=('two.radical-project.org', 33162))
runner.add_protocol(sim)
runner.run(walltime=1440, queue='high', access_schema='local')