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import openmm as mm
import openmm.unit as unit
from openmm import app
from openmmtools.integrators import VVVRIntegrator
from potentials.MoleculePotential import MoleculePotential
class PolyPotentialMD(MoleculePotential):
def __init__(self, start_file, index, reset_steps=100, save_file=None):
super().__init__(start_file, index, reset_steps, save_file)
def setup(self):
pdb = app.PDBFile(self.start_file)
forcefield = app.ForceField('amber/protein.ff14SBonlysc.xml',
'implicit/gbn2.xml')
system = forcefield.createSystem(
pdb.topology,
nonbondedMethod=app.NoCutoff,
nonbondedCutoff=1.0 * unit.nanometers,
constraints=app.HBonds,
rigidWater=True,
ewaldErrorTolerance=0.0005
)
external_force = mm.CustomExternalForce("k*(fx*x + fy*y + fz*z)")
# creating the parameters
external_force.addGlobalParameter("k", 1000)
external_force.addPerParticleParameter("fx")
external_force.addPerParticleParameter("fy")
external_force.addPerParticleParameter("fz")
system.addForce(external_force)
for i in range(len(pdb.positions)):
external_force.addParticle(i, [0, 0, 0])
integrator = VVVRIntegrator(
300 * unit.kelvin, # temp
1.0 / unit.picoseconds, # collision rate
2.0 * unit.femtoseconds) # timestep
integrator.setConstraintTolerance(0.00001)
platform = mm.Platform.getPlatformByName('CUDA')
properties = {'DeviceIndex': '0', 'Precision': 'mixed'}
simulation = app.Simulation(pdb.topology, system, integrator,
platform, properties)
simulation.context.setPositions(pdb.positions)
return pdb, simulation, external_force
def get_position_file(self):
return f"{self.save_file}/PolyPositions"
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