mockup python file: InterAtomicReporter.py
test of md simulation with InterAtomicReporter reporter: test/try_mockup.py
Goal image
# Input Files
pdb = PDBFile('input/7r98-processed.pdb')
forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
# Some Configuration
# ...
# Prepare the Simulation
topology = pdb.topology
positions = pdb.positions
system = forcefield.createSystem(topology, nonbondedMethod=nonbondedMethod, nonbondedCutoff=nonbondedCutoff,
constraints=constraints, rigidWater=rigidWater, ewaldErrorTolerance=ewaldErrorTolerance)
system.addForce(MonteCarloBarostat(pressure, temperature, barostatInterval))
integrator = LangevinMiddleIntegrator(temperature, friction, dt)
integrator.setConstraintTolerance(constraintTolerance)
simulation = Simulation(topology, system, integrator, platform, platformProperties)
simulation.context.setPositions(positions)
# Minimize and Equilibrate
simulation.minimizeEnergy()
simulation.context.setVelocitiesToTemperature(temperature)
simulation.step(equilibrationSteps)
# Simulate
simulation.reporters.append(HeatFluxReporter(outpath="out/heat_flux.nc", interval=1000, decomp=True, cutoff=1.0*nanometer))
simulation.currentStep = 0
simulation.step(steps)