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16 lines
733 B
Python
16 lines
733 B
Python
from openmm.app import *
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from openmm import *
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from openmm.unit import *
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from sys import stdout
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inpcrd = AmberInpcrdFile('input.inpcrd')
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prmtop = AmberPrmtopFile('input.prmtop', periodicBoxVectors=inpcrd.boxVectors)
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system = prmtop.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
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integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
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simulation = Simulation(prmtop.topology, system, integrator)
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simulation.context.setPositions(inpcrd.positions)
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simulation.minimizeEnergy()
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simulation.reporters.append(DCDReporter('output.dcd', 1000))
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simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True))
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simulation.step(10000)
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