Anisotropic_CG_ConjPoly_Model/in_3sc.initialize at main · TheJacksonLab/Anisotropic_CG_ConjPoly_Model · GitHub

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#trying to just see how one polymer chain moves

dimension	3
units 		lj
atom_style	hybrid full ellipsoid
boundary 	p p p

bond_style	hybrid harmonic eldihedral

angle_style 	harmonic
dihedral_style	none
improper_style	none

pair_style hybrid gayberne 1.0 1.0 1.0 3.0 lj/cut 3.0
fix prop all property/atom i_coreid
read_data "v5_sidechains.data" fix prop NULL CoreIDs

special_bonds lj 0.0 1.0 1.0

pair_coeff 1 1 gayberne 1.0 1.0 0.1 1.0 0.25 0.1 1.0 0.25
pair_coeff 2 2 gayberne 0.0 1.0 1 1 1 1 1 1
pair_coeff * 2 gayberne 0 1.0 0 0 0 0 0 0
pair_coeff 3 3 lj/cut 0.01 0.25
pair_coeff 1 3 lj/cut 0.01 0.72
pair_coeff 2 3 lj/cut 0 1.0

bond_coeff 1 harmonic 0.0 0.5
bond_coeff 2 harmonic 200.0 0.2
bond_coeff 3 eldihedral 0 3.0 0 0
bond_coeff 4 harmonic 200.0 0.2
bond_coeff 5 harmonic 0.0 0.36

angle_coeff 1 3.0 180.0
angle_coeff 2 1.0 180.0

group disks type 1 2

group ell type 1
group bondSites type 2
group sideChains type 3
group real type 1 3

neigh_modify delay 1 exclude group ell bondSites

fix 1 disks rigid/nve/small custom i_coreid
fix 2 ell langevin 1.5 1.5 2 1 angmom 1.0
fix 3 sideChains nve
fix 4 sideChains langevin 1.5 1.5 2 1
fix drift all momentum 10000 linear 1 1 1 angular rescale

restart 1000000 restarts/equil.*.rst

compute ta ell temp/asphere dof all
compute rot all erotate/rigid 1
compute kin all ke/rigid 1

compute op real property/atom quati quatj quatk quatw
compute shape real property/atom shapex shapey shapez
dump 1 real custom 100000 ovito.dump id type xu yu zu c_op[1] c_op[2] c_op[3] c_op[4] c_shape[1] c_shape[2] c_shape[3]

timestep 0.001

thermo_style custom step temp c_ta epair ebond eangle etotal press pe ke c_rot c_kin lx ly lz

thermo 25000

run 20000000