def test_integrator_decorators():
integrator = integrators.HMCIntegrator(timestep=0.05 * unit.femtoseconds)
testsystem = testsystems.IdealGas()
nsteps = 25
context = openmm.Context(testsystem.system, integrator)
context.setPositions(testsystem.positions)
context.setVelocitiesToTemperature(300 * unit.kelvin)
integrator.step(nsteps)
assert integrator.n_accept == nsteps
assert integrator.n_trials == nsteps
assert integrator.acceptance_rate == 1.0
import openmmtools.testsystems
from openmmtools import testsystems
from pymbar import timeseries
from functools import partial
from openmmmcmc.mcmc import HMCMove, GHMCMove, LangevinDynamicsMove, MonteCarloBarostatMove
import logging
# Test various combinations of systems and MCMC schemes
analytical_testsystems = [
("HarmonicOscillator", testsystems.HarmonicOscillator(), [ GHMCMove(timestep=10.0*units.femtoseconds,nsteps=100) ]),
("HarmonicOscillator", testsystems.HarmonicOscillator(), { GHMCMove(timestep=10.0*units.femtoseconds,nsteps=100) : 0.5, HMCMove(timestep=10*units.femtosecond, nsteps=10) : 0.5 }),
("HarmonicOscillatorArray", testsystems.HarmonicOscillatorArray(N=4), [ LangevinDynamicsMove(timestep=10.0*units.femtoseconds,nsteps=100) ]),
("IdealGas", testsystems.IdealGas(nparticles=216), [ HMCMove(timestep=10*units.femtosecond, nsteps=10), MonteCarloBarostatMove() ])
]
NSIGMA_CUTOFF = 6.0 # cutoff for significance testing
debug = False # set to True only for manual debugging of this nose test
def test_minimizer_all_testsystems():
#testsystem_classes = testsystems.TestSystem.__subclasses__()
testsystem_classes = [ testsystems.AlanineDipeptideVacuum ]
for testsystem_class in testsystem_classes:
class_name = testsystem_class.__name__
logging.info("Testing minimization with testsystem %s" % class_name)
testsystem = testsystem_class()
# =============================================================================
# GLOBAL TEST CONSTANTS
# =============================================================================
# Test various combinations of systems and MCMC schemes
analytical_testsystems = [
("HarmonicOscillator", testsystems.HarmonicOscillator(),
GHMCMove(timestep=10.0 * unit.femtoseconds, n_steps=100)),
("HarmonicOscillator", testsystems.HarmonicOscillator(),
WeightedMove([(GHMCMove(timestep=10.0 * unit.femtoseconds,
n_steps=100), 0.5),
(HMCMove(timestep=10 * unit.femtosecond,
n_steps=10), 0.5)])),
("HarmonicOscillatorArray", testsystems.HarmonicOscillatorArray(N=4),
LangevinDynamicsMove(timestep=10.0 * unit.femtoseconds, n_steps=100)),
("IdealGas", testsystems.IdealGas(nparticles=216),
SequenceMove([
HMCMove(timestep=10 * unit.femtosecond, n_steps=10),
MonteCarloBarostatMove()
]))
]
NSIGMA_CUTOFF = 6.0 # cutoff for significance testing
debug = True # set to True only for manual debugging of this nose test
# =============================================================================
# TEST FUNCTIONS
# =============================================================================
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from openmmtools import integrators, testsystems
import os
import sys
from sys import stdout
argon = testsystems.IdealGas()
########################################################################
# Datos a modificar para las simulaciones
cutoff = 206.227 * 0.5 # en nm
ensamble = "NVE" # tipos: NVE, NVT, NPT
dt = 0.002 # picosegundos
T = 298.0 # kelvin
P = 1.0 # atmosferas
intervaloBarost = 25 # frecuencia de activacion del barostato
stepImp = 50 # frecuencia de impresion (adimensional)
pasosTotales = 1000 # este valor por stepImp por dt da la longitud de la trayectoria
VelocityVerlet = False # Solo para NVE ponerlo en True
########################################################################
system = argon.system
if ensamble == "NVE":
if VelocityVerlet == True:
# utilizando openmmtools
integrator = integrators.VelocityVerletIntegrator(dt * picoseconds)
integrator.addConstrainPositions()
integrator.addConstrainVelocities()