from adaptivemd.engine.openmm import OpenMMEngine
from adaptivemd.analysis.pyemma import PyEMMAAnalysis
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcaseallegro')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
# resource_id = 'fub.allegro'
project.initialize(AllegroCluster())
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../files/alanine/alanine.pdb').named(
'initial_pdb').load()
engine = OpenMMEngine(
pdb_file=pdb_file,
system_file=File('file://../files/alanine/system.xml').load(),
integrator_file=File('file://../files/alanine/integrator.xml').load(),
args='-r --report-interval 10 --store-interval 1 -p CPU').named(
'openmm')
elif len(sys.argv) == 2:
resource_id = sys.argv[1]
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
if resource_id == 'local.jhp':
resource = LocalResource(15, 2)
resource.add_path(amp.path_conda_local_jhp)
elif resource_id == 'local.sheep':
resource = LocalResource(15, 2)
resource.add_path(amp.path_conda_local_sheep)
elif resource_id == 'fub.allegro':
resource = AllegroCluster(15, 4, 'big')
resource.add_path(amp.path_conda_allegro_jhp)
else:
resource = LocalResource(1, 2)
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://input.pdb')
engine = OpenMMEngine(pdb_file=pdb_file,
system_file=File('file://system.xml'),
integrator_file=File('file://integrator.xml'))
engine.args = '-r --report-interval 1 -p fastest --store-interval 1'
from adaptivemd import AllegroCluster
from adaptivemd import OpenMMEngine
from adaptivemd import File
if __name__ == '__main__':
project = Project('testcase')
# --------------------------------------------------------------------------
# CREATE THE RESOURCE
# the instance to know about the place where we run simulations
# --------------------------------------------------------------------------
resource = AllegroCluster()
project.initialize(resource)
# --------------------------------------------------------------------------
# CREATE THE ENGINE
# the instance to create trajectories
# --------------------------------------------------------------------------
pdb_file = File('file://../files/alanine/alanine.pdb').named('initial_pdb')
engine = OpenMMEngine(
pdb_file=pdb_file,
system_file=File('file://../files/alanine/system.xml'),
integrator_file=File('file://../files/alanine/integrator.xml'),
args='-r --report-interval 1 --store-interval 1 -p CUDA').named(
'openmm')