# WCA between monomers
system.non_bonded_inter[0, 0].wca.set_params(epsilon=1, sigma=1)
# WCA counter-ions - polymer
system.non_bonded_inter[0, 1].wca.set_params(epsilon=1, sigma=1)
# WCA ions - polymer
system.non_bonded_inter[0, 2].wca.set_params(epsilon=1, sigma=1)
# WCA between ions
system.non_bonded_inter[1, 2].wca.set_params(epsilon=1, sigma=1)
# bonded interactions
################################################################
harmonic_bond = interactions.HarmonicBond(k=10, r_0=2)
angle_harmonic_bond = interactions.AngleHarmonic(bend=10, phi0=np.pi)
system.bonded_inter.add(harmonic_bond)
system.bonded_inter.add(angle_harmonic_bond)
# create monomer beads and bonds
##########################################################################
init_polymer_pos = espressomd.polymer.linear_polymer_positions(
n_polymers=1,
beads_per_chain=N_MONOMERS,
bond_length=2.0,
seed=2,
bond_angle=np.pi,
min_distance=1.8,
start_positions=np.array([system.box_l / 2.0]))
system.part.add(pos=init_polymer_pos[0], q=-np.ones(N_MONOMERS))
# WCA ions - polymer
system.non_bonded_inter[0, 2].wca.set_params(
epsilon=1, sigma=1)
# WCA between ions
system.non_bonded_inter[1, 2].wca.set_params(
epsilon=1, sigma=1)
# Bonded interactions
################################################################
# fene = interactions.FeneBond(k=10, d_r_max=2)
# system.bonded_inter.add(fene)
harmonic = interactions.HarmonicBond(k=10, r_0=2)
harmonicangle = interactions.AngleHarmonic(bend=10, phi0=np.pi)
system.bonded_inter.add(harmonic)
system.bonded_inter.add(harmonicangle)
# Create Monomer beads and bonds
#########################################################################################
n_monomers = 20
init_polymer_pos = np.dstack(
(np.arange(n_monomers), np.zeros(n_monomers), np.zeros(n_monomers)))[0] + \
np.array([system.box_l[0] / 2 - n_monomers / 2,
system.box_l[1] / 2,
system.box_l[2] / 2])
system.part.add(pos=init_polymer_pos)