Dear,
When I do coarse-gained bead spring model of polyelectrolyte(PE), I get the result that the distance of monomer -monomer ,cation- cation and others is shorter than 0.1.
I simulate the LJ liquid system with a polymer. There are 20000 particles and density is about 0.8, and reduced temperature is 1.0 maintained by Nose-hoover thermostat. The charge of PE monomer is -0.8, coion is +/ - 1. The distance and code are as follows.
Is the result right? What does it matter? Could some experts give me a hand?
Thanks in advance!
ID ID distance
PE monomer
0 2 0.0529925
14 16 0.114295
29 31 0.073276
34 36 0.110236
cation
28 85 0.00704945
41 44 0.00883346
65 133 0.0185814
94 109 0.0121244
102 137 0.071066
107 114 0.0218238
107 128 0.0462458
110 117 0.0489235
114 128 0.0680696
115 131 0.0983805
MY code:
units lj
dimension 3
boundary p p p
neighbor 0.5 bin
neigh_modify every 1 delay 3 check yes
atom_style full
bond_style fene/expand
special_bonds 0 1 1
read_data 08.data
group poly type 1
group ion type 2 3
group system type 1 2 3
group water type 4
bond_coeff 1 30.0 1.5 1.0 1.0 0.0
pair_style hybrid/overlay lj/cut 1.12246 coul/long 6.0
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 13 13 coul/long
dielectric 0.5405
pair_modify shift yes
kspace_style pppm 0.000001
timestep 0.005
velocity all create 1.0 999898 dist gaussian units box
fix 1 all nvt 1.0 1.0 0.5
thermo 500
run 200000
write_restart restart.equ
Step Temp E_pair E_mol TotEng Press
0 0.99704038 0.81833312 0.031434147 2.3452811 6.5884937
500 0.9963951 0.81855194 0.031583804 2.3446817 6.5903531
1000 0.99987604 0.81464423 0.031624837 2.3460363 6.5781232
1500 0.99392023 0.82109146 0.031724534 2.3436498 6.6015723
2000 0.99021621 0.82286112 0.031558641 2.3396977 6.6084199
2500 1.0036663 0.8063814 0.031484399 2.3433183 6.5340965
3000 0.99655956 0.81731761 0.031690784 2.343801 6.5944441
3500 1.0002421 0.81375398 0.03154936 2.3456197 6.5740961
4000 1.0023508 0.81523634 0.031606401 2.3503219 6.5715586
4500 1.0033047 0.82031823 0.031745938 2.3569742 6.6202197
5000 1.0025156 0.82153028 0.031803728 2.3570605 6.6182736
5500 1.0031065 0.81594562 0.031623089 2.3521815 6.590568
6000 1.0020242 0.81995464 0.031487439 2.3544314 6.6090816
6500 0.99823633 0.81878782 0.031733504 2.347829 6.5955382
7000 1.0046896 0.81458972 0.031614211 2.3531912 6.5827166
…