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| using PyCall | ||
| import ISOKANN: propagate | ||
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| py""" | ||
| from openmm.app import * | ||
| from openmm import * | ||
| from openmm.unit import * | ||
| from sys import stdout | ||
| """ | ||
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| nanometer = py"nanometer" | ||
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| struct OpenMMSimulation | ||
| pysim::PyObject | ||
| steps::Int | ||
| end | ||
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| ### | ||
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| function propagate(sim::OpenMMSimulation, x0) | ||
| steps = sim.steps | ||
| pysim = sim.pysim | ||
| setcoords(pysim, x0) | ||
| pysim.step(steps) | ||
| getcoords(pysim) | ||
| end | ||
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| function propagate(sim::OpenMMSimulation, x0::AbstractMatrix, ny) | ||
| dim, nx = size(x0) | ||
| ys = zeros(dim, nx, ny) | ||
| for i in 1:nx, j in 1:ny | ||
| ys[:, i, j] = propagate(sim, x0[:, i]) | ||
| end | ||
| return ys | ||
| end | ||
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| function getcoords(sim::PyObject) | ||
| x = sim.context.getState(getPositions=true).getPositions().value_in_unit(nanometer) | ||
| reinterpret(Float64, x) | ||
| end | ||
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| function setcoords(sim::PyObject, coords) | ||
| x = reinterpret(Tuple{Float64,Float64,Float64}, coords) * nanometer | ||
| sim.context.setPositions(x) | ||
| end | ||
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| ### | ||
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| function openmm_examplesys(; | ||
| temp=300, | ||
| friction=1, | ||
| step=0.004, | ||
| pdb="/home/htc/bzfsikor/.julia/conda/3/share/openmm/examples/input.pdb", | ||
| forcefields=["amber14-all.xml", "amber14/tip3pfb.xml"], | ||
| steps=100) | ||
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| py""" | ||
| pdb = PDBFile($pdb) | ||
| forcefield = ForceField(*$forcefields) | ||
| system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, | ||
| nonbondedCutoff=1*nanometer, constraints=HBonds) | ||
| integrator = LangevinMiddleIntegrator($temp*kelvin, $friction/picosecond, $step*picoseconds) | ||
| simulation = Simulation(pdb.topology, system, integrator) | ||
| simulation.context.setPositions(pdb.positions) | ||
| """ | ||
| # simulation.minimizeEnergy() | ||
| # simulation.reporters.append(PDBReporter('output.pdb', 1000)) | ||
| # simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, | ||
| # potentialEnergy=True, temperature=True)) | ||
| # simulation.step(10000) | ||
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| sim = py"simulation" | ||
| return OpenMMSimulation(sim, steps) | ||
| end | ||
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| ### | ||
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| function test_getsetcoords(sim) | ||
| x = getcoords(sim) | ||
| bak = copy(x) | ||
| setcoords(sim, x) | ||
| @assert getcoords(sim) == bak | ||
| end |