def make_toy_system_object(model):
"""
Make openmm system and topology files for use with a toy system.
"""
system = openmm.System()
topology = openmm_app.Topology()
num_particles = model.toy_settings.num_particles
assert model.toy_settings.num_particles == len(model.toy_settings.masses)
new_expression = "k*(" + model.toy_settings.potential_energy_expression + ")"
force = openmm.CustomCentroidBondForce(num_particles, new_expression)
force.addGlobalParameter("k", 1.0 * openmm.unit.kilocalories_per_mole)
groups_list = []
for i in range(num_particles):
mass = model.toy_settings.masses[i] * openmm.unit.amu
system.addParticle(mass)
atom_name = "X{}".format(i)
if not atom_name in openmm_app.element.Element._elements_by_symbol:
element = openmm_app.element.Element(0, atom_name, atom_name, mass)
else:
element = openmm_app.element.Element._elements_by_symbol[atom_name]
chain = topology.addChain()
residue = topology.addResidue("UNK", chain)
topology.addAtom(atom_name, element, residue)
groups_list.append(force.addGroup([i]))
force.addBond(groups_list, [])
system.addForce(force)
return system, topology
def make_fwd_rev_force_object(self):
"""
Make a list of reversal force objects, which will be used to
monitor milestone crossing during the reversal stage.
"""
try:
import openmm
except ImportError:
import simtk.openmm as openmm
return openmm.CustomCentroidBondForce(
self.num_groups, self.openmm_fwd_rev_expression)
def make_umbrella_force_object(self):
"""
Make an umbrella sampling force object, which will constrain
the system to the milestone.
"""
try:
import openmm
except ImportError:
import simtk.openmm as openmm
return openmm.CustomCentroidBondForce(
self.num_groups, self.openmm_umbrella_expression)
def make_force_object(self):
"""
Create an OpenMM force object which will be used to compute
the value of the CV's mathematical expression as the simulation
propagates. Each *milestone* in a cell, not each CV, will have
a force object created.
In this implementation of MMVT in OpenMM, CustomForce objects
are used to provide the boundary definitions of the MMVt cell.
These 'forces' are designed to never affect atomic motions,
but are merely monitored by the plugin for bouncing event.
So while they are technically OpenMM force objects, we don't
refer to them as forces outside of this layer of the code,
preferring instead the term: boundary definitions.
"""
try:
import openmm
except ImportError:
import simtk.openmm as openmm
assert self.num_groups == 2
return openmm.CustomCentroidBondForce(self.num_groups,
self.openmm_expression)
# (s.atom_list['residue_index'] == 999)]
A2 = coord.getPositions()[-1]
Z_A2 = A2[2]
external_force2.addGlobalParameter('k_spring', 10)
external_force2.addGlobalParameter('x_A2', A2[0])
external_force2.addGlobalParameter('y_A2', A2[1])
external_force2.addGlobalParameter('Z_A2', A2[2])
external_force2.addParticle(int(s.atom_list.index[-1]))
external_force.setForceGroup(10)
external_force2.setForceGroup(10)
s.system.addForce(external_force)
s.system.addForce(external_force2)
#Add bond between pulling particle and the com of the pulled particles
centroid_force = openmm.CustomCentroidBondForce(2,
"0.5*k*distance(g1,g2)^2")
centroid_force.addPerBondParameter("k")
centroid_force.addGroup([int(a) for a in A_index])
centroid_force.addGroup([int(a) for a in B_index])
centroid_force.addGroup([int(s.atom_list.index[-2])]) # A
centroid_force.addGroup([int(s.atom_list.index[-1])]) # B
centroid_force.addBond([0, 2], [1]) # A
centroid_force.addBond([1, 3], [1]) # B
centroid_force.setForceGroup(11)
s.system.addForce(centroid_force)
# Set up simulation
temperature = sjob["temperature"] * u.kelvin
integrator = openmm.LangevinIntegrator(temperature, .0001 / u.picosecond,
1 * u.picoseconds)
simulation = openmm.app.Simulation(top.topology, s.system, integrator,