Hello,
I am using Lammps to simulate DNA electrophoresis. In the adsorption process( I am using single chain and it should adsorb to the substrate by interaction between molecules.), but this WARNING appears every time in the equilibrium process or when it touches the substrate. then the chain breaks. Below is my in. file.
Could you help me find out the problem??
#3d electrophoresis
1. create wall
units lj
dimension 3
atom_style hybrid charge bond
boundary p p p
neighbor 0.4 bin
neigh_modify every 1 delay 1
read_data data.newdata
bond_style fene
bond_coeff 1 30 1.5 1.0 1.0
special_bonds fene
#create geometry
lattice fcc 13.6 orient x 1 -2 1 orient y 1 0 -1 orient z 1 1 1
#lattice fcc 6.8 orient x 1 -2 1 orient y 1 0 -1 orient z 1 1 1
region Simbox block 0 100 0 100 0 100
#atom regions
region stripe1 block 0 50 0 70 0 0.5 units lattice
create_atoms 2 region stripe1
group wall-1 type 2
group wall union wall-1
group moving type 1
#L-J potential
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1 1
pair_coeff 1 2 2.5 1
2.initial velocities
fix 1 all nvt temp 1 1 1
fix 3 all langevin 1.0 1.0 10.0 101
fix 5 wall setforce 0 0 0
Run
timestep 0.005
thermo 100
dump 3 all xyz 100 testfile.xyz
dump_modify 3 sort id
run 18500
Small system test
61 atoms
60 bonds
0 angles
0 dihedrals
0 impropers
2 atom types
1 bond types
0 angle types
0 dihedral types
0 improper types
0 100 xlo xhi
0 95 ylo yhi
0 100 zlo zhi
Masses
1 1
2 1
Atoms
1 1 17.97 26.00 22.00 1.00 1
2 1 18.94 26.00 22.00 1.00 1
3 1 19.91 26.00 22.00 1.00 1
4 1 20.88 26.00 22.00 1.00 1
5 1 21.85 26.00 22.00 1.00 1
6 1 22.82 26.00 22.00 1.00 1
7 1 23.79 26.00 22.00 1.00 1
8 1 24.76 26.00 22.00 1.00 1
9 1 25.73 26.00 22.00 1.00 1
10 1 26.70 26.00 22.00 1.00 1
11 1 27.67 26.00 22.00 1.00 1
12 1 28.64 26.00 22.00 1.00 1
13 1 29.61 26.00 22.00 1.00 1
14 1 30.58 26.00 22.00 1.00 1
15 1 31.55 26.00 22.00 1.00 1
16 1 32.52 26.00 22.00 1.00 1
17 1 33.49 26.00 22.00 1.00 1
18 1 34.46 26.00 22.00 1.00 1
19 1 35.43 26.00 22.00 1.00 1
20 1 36.40 26.00 22.00 1.00 1
21 1 37.37 26.00 22.00 1.00 1
22 1 38.34 26.00 22.00 1.00 1
23 1 39.31 26.00 22.00 1.00 1
24 1 40.28 26.00 22.00 1.00 1
25 1 41.25 26.00 22.00 1.00 1
26 1 42.22 26.00 22.00 1.00 1
27 1 43.19 26.00 22.00 1.00 1
28 1 44.16 26.00 22.00 1.00 1
29 1 45.13 26.00 22.00 1.00 1
30 1 46.10 26.00 22.00 1.00 1
31 1 46.10 27.00 22.00 1.00 1
32 1 45.13 27.00 22.00 1.00 1
33 1 44.16 27.00 22.00 1.00 1
34 1 43.19 27.00 22.00 1.00 1
35 1 42.22 27.00 22.00 1.00 1
36 1 41.25 27.00 22.00 1.00 1
37 1 40.28 27.00 22.00 1.00 1
38 1 39.31 27.00 22.00 1.00 1
39 1 38.34 27.00 22.00 1.00 1
40 1 37.37 27.00 22.00 1.00 1
41 1 36.40 27.00 22.00 1.00 1
42 1 35.43 27.00 22.00 1.00 1
43 1 34.46 27.00 22.00 1.00 1
44 1 33.49 27.00 22.00 1.00 1
45 1 32.52 27.00 22.00 1.00 1
46 1 31.55 27.00 22.00 1.00 1
47 1 30.58 27.00 22.00 1.00 1
48 1 29.61 27.00 22.00 1.00 1
49 1 28.64 27.00 22.00 1.00 1
50 1 27.67 27.00 22.00 1.00 1
51 1 26.70 27.00 22.00 1.00 1
52 1 25.73 27.00 22.00 1.00 1
53 1 24.76 27.00 22.00 1.00 1
54 1 23.79 27.00 22.00 1.00 1
55 1 22.82 27.00 22.00 1.00 1
56 1 21.85 27.00 22.00 1.00 1
57 1 20.88 27.00 22.00 1.00 1
58 1 19.91 27.00 22.00 1.00 1
59 1 18.94 27.00 22.00 1.00 1
60 1 17.97 27.00 22.00 1.00 1
61 1 17.97 28.00 23.00 1.00 1
Bonds
1 1 1 2
2 1 2 3
3 1 3 4
4 1 4 5
5 1 5 6
6 1 6 7
7 1 7 8
8 1 8 9
9 1 9 10
10 1 10 11
11 1 11 12
12 1 12 13
13 1 13 14
14 1 14 15
15 1 15 16
16 1 16 17
17 1 17 18
18 1 18 19
19 1 19 20
20 1 20 21
21 1 21 22
22 1 22 23
23 1 23 24
24 1 24 25
25 1 25 26
26 1 26 27
27 1 27 28
28 1 28 29
29 1 29 30
30 1 30 31
31 1 31 32
32 1 32 33
33 1 33 34
34 1 34 35
35 1 35 36
36 1 36 37
37 1 37 38
38 1 38 39
39 1 39 40
40 1 40 41
41 1 41 42
42 1 42 43
43 1 43 44
44 1 44 45
45 1 45 46
46 1 46 47
47 1 47 48
48 1 48 49
49 1 49 50
50 1 50 51
51 1 51 52
52 1 52 53
53 1 53 54
54 1 54 55
55 1 55 56
56 1 56 57
57 1 57 58
58 1 58 59
59 1 59 60
60 1 60 61
Best regards,
Chao