34 lines
1.2 KiB
Plaintext
34 lines
1.2 KiB
Plaintext
# Charge regulation lammps for a polymer chain
|
|
units lj
|
|
atom_style full
|
|
neighbor 3.0 bin
|
|
read_data data.chreg-polymer
|
|
|
|
bond_style harmonic
|
|
bond_coeff 1 100 1.122462 # K R0
|
|
velocity all create 1.0 8008 loop geom
|
|
|
|
pair_style lj/cut/coul/long 1.122462 20
|
|
pair_coeff * * 1.0 1.0 1.122462 # charges
|
|
kspace_style pppm 1.0e-3
|
|
pair_modify shift yes
|
|
dielectric 1.0
|
|
|
|
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
|
fix fnve all nve
|
|
compute dtemp all temp
|
|
compute_modify dtemp dynamic yes
|
|
fix fT all langevin 1.0 1.0 1.0 123
|
|
fix_modify fT temp dtemp
|
|
|
|
fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
|
|
fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
|
|
fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
|
|
|
|
thermo 100
|
|
# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
|
|
thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
|
|
|
timestep 0.005
|
|
run 2000
|