Add forbidden z region#
import molsysmt as msm
import openmm as mm
from openmm import unit
from openmm import app
from tqdm import tqdm
import numpy as np
from matplotlib import pyplot as plt
system = mm.System()
system.addParticle(39.948 * unit.amu) # masa del átomo de argón
0
msm.thirds.openmm.forces.add_forbidden_z_region(system, z0='1.0 nm', width='1.5 nm',
force_constant = '5000 kilojoules/(mol*angstroms**2)',
pbc=True)
0
# Formalismo NVT
temperature = 300*unit.kelvin
integration_timestep = 2.0*unit.femtoseconds
saving_timestep = 1.00*unit.picoseconds
simulation_time = 1000.*unit.picoseconds
saving_steps = int(saving_timestep/integration_timestep)
num_saving_steps = int(simulation_time/saving_timestep)
friction = 5.0/unit.picoseconds
integrator = mm.LangevinIntegrator(temperature, friction, integration_timestep)
platform = mm.Platform.getPlatformByName('OpenCL')
times = np.zeros(num_saving_steps, np.float32) * unit.picoseconds
positions = np.zeros([num_saving_steps,3], np.float32) * unit.nanometers
velocities = np.zeros([num_saving_steps,3], np.float32) * unit.nanometers/unit.picosecond
potential_energies = np.zeros([num_saving_steps], np.float32) * unit.kilocalories_per_mole
kinetic_energies = np.zeros([num_saving_steps], np.float32) * unit.kilocalories_per_mole
initial_positions = [[0.0, 0.0, 2.0]] * unit.nanometers
context = mm.Context(system, integrator, platform)
context.setPositions(initial_positions)
L = 2.0
v1 = [L,0,0] * unit.nanometers
v2 = [0,L,0] * unit.nanometers
v3 = [0,0,L] * unit.nanometers
L = L * unit.nanometers
context.setPeriodicBoxVectors(v1, v2, v3)
state = context.getState(getEnergy=True, getPositions=True, getVelocities=True)
times[0] = state.getTime()
positions[0] = state.getPositions()[0]
velocities[0] = state.getVelocities()[0]
kinetic_energies[0]=state.getKineticEnergy()
potential_energies[0]=state.getPotentialEnergy()
for ii in tqdm(range(1,num_saving_steps)):
context.getIntegrator().step(saving_steps)
state_xx = context.getState(getEnergy=True, getPositions=True, getVelocities=True)
times[ii] = state_xx.getTime()
positions[ii] = state_xx.getPositions()[0]
velocities[ii] = state_xx.getVelocities()[0]
kinetic_energies[ii]=state_xx.getKineticEnergy()
potential_energies[ii]=state_xx.getPotentialEnergy()
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98%|█████████▊| 977/999 [00:51<00:01, 19.15it/s]
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100%|██████████| 999/999 [00:52<00:00, 17.95it/s]
100%|██████████| 999/999 [00:52<00:00, 18.98it/s]
plt.plot(times, positions[:,2])
plt.axhline(y=2.25, color='red', linestyle='-')
plt.axhline(y=1.75, color='red', linestyle='-')
plt.show()
