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