Dear,
When I follow an excellent MD simulition work with Lammps, I was given an errors “FENE bond too long”.
I don’t know how to deal with it, though manual gives some notice. I have tried a lot of methods, such as changing atoms’coordinates ,bond parameter. I hope some kind person help me analyse the reasons and give me some advice.
I have posted the in.file and data.file, parameters are the same as the followed article.
Thanks in advance.
in.luo
Bead-spring polymer simulation of polymer through a pore
use soft potential to un-overlap
echo screen
units lj
dimension 2
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 5 check yes
atom_style full
bond_style fene/expand
special_bonds 0.0 1.0 1.0
read_data data.luoprl
group dna type 1
group wall type 2 3
velocity dna create 1.2 23456
bond_coeff 1 7 2 1.0 1.0 0.0
timestep 0.01
Soft peotential push-off
pair_style soft 2.0
pair_coeff * * 0.0 0.0
pair_coeff 1 1 1.0 30.0
pair_coeff 1 2 1.0 30.0
fix 1 dna nve
fix 2 dna langevin 1.5 1.2 0.7 23456
fix 3 all enforce2d
fix 4 wall setforce 0.0 0.0 0.0
thermo 100
dump 1 all atom 100 soft.all
run 10000
#Main run
undump 1
reset_timestep 0
pair_style lj/cut 1.2246
pair_coeff * * 1.0 1.0
pair_coeff 1 3 1.0 1.0 2.5
pair_modify shift yes
fix 2 dna langevin 1.2 1.2 0.7 45678
fix 5 dna addforce 1.0 0.0 0.0
thermo 5000
dump 2 dna atom 100 dump.dna
dump 3 all atom 100 dump.all
restart 5000 restart.%.dna
run 500000
data.luoprl
LAMMPS Description
162 atoms
127 bonds
0 angles
0 dihedrals
0 impropers
3 atom types
1 bond types
0 angle types
0 dihedral types
0 improper types
-15.0005 5.0005 xlo xhi
-8.0005 8.0005 ylo yhi
-0.0505 0.0505 zlo zhi
Masses
1 1
2 1
3 1
Atoms
1 1 1 0 -2 0 0.0 0 0 0
2 1 1 0 -2.76711 -0.52565 0.0 0 0 0
3 1 1 0 -3.76154 0.405511 0.0 0 0 0
4 1 1 0 -4.6318 0.0784557 0.0 0 0 0
5 1 1 0 -5.62439 0.775708 0.0 0 0 0
6 1 1 0 -6.55581 1.55841 0.0 0 0 0
7 1 1 0 -5.56041 2.54406 0.0 0 0 0
8 1 1 0 -5.83678 3.26817 0.0 0 0 0
9 1 1 0 -6.7718 4.2635 0.0 0 0 0
10 1 1 0 -7.76443 3.26419 0.0 0 0 0
11 1 1 0 -7.39927 2.28558 0.0 0 0 0
12 1 1 0 -7.15769 1.31761 0.0 0 0 0
13 1 1 0 -7.98986 0.358031 0.0 0 0 0
14 1 1 0 -8.98625 1.2598 0.0 0 0 0
15 1 1 0 -9.98056 2.25818 0.0 0 0 0
16 1 1 0 -10.1247 2.53892 0.0 0 0 0
17 1 1 0 -10.9856 3.53873 0.0 0 0 0
18 1 1 0 -10.964 4.44649 0.0 0 0 0
19 1 1 0 -11.4962 5.06777 0.0 0 0 0
20 1 1 0 -12.4115 5.84162 0.0 0 0 0
21 1 1 0 -13.392 6.31016 0.0 0 0 0
22 1 1 0 -14.3855 5.55027 0.0 0 0 0
23 1 1 0 -13.3855 4.56247 0.0 0 0 0
24 1 1 0 -13.2194 4.26549 0.0 0 0 0
25 1 1 0 -12.2417 3.26585 0.0 0 0 0
26 1 1 0 -11.3363 4.26584 0.0 0 0 0
27 1 1 0 -10.4302 4.68246 0.0 0 0 0
28 1 1 0 -9.70211 5.68175 0.0 0 0 0
29 1 1 0 -8.79207 6.56452 0.0 0 0 0
30 1 1 0 -7.84598 7.55409 0.0 0 0 0
31 1 1 0 -6.84607 6.56213 0.0 0 0 0
32 1 1 0 -6.39482 6.72122 0.0 0 0 0
33 1 1 0 -5.39784 5.88892 0.0 0 0 0
34 1 1 0 -6.16223 4.88965 0.0 0 0 0
35 1 1 0 -6.59916 3.89002 0.0 0 0 0
36 1 1 0 -7.58468 3.5752 0.0 0 0 0
37 1 1 0 -8.34171 4.20229 0.0 0 0 0
38 1 1 0 -7.34315 5.18589 0.0 0 0 0
39 1 1 0 -6.34338 5.20542 0.0 0 0 0
40 1 1 0 -5.89023 5.60636 0.0 0 0 0
41 1 1 0 -4.93767 6.4337 0.0 0 0 0
42 1 1 0 -5.5116 7.28 0.0 0 0 0
43 1 1 0 -6.49583 -7.73304 0.0 0 1 0
44 1 1 0 -7.47973 -7.8052 0.0 0 1 0
45 1 1 0 -6.49558 7.22703 0.0 0 0 0
46 1 1 0 -7.47612 -7.77577 0.0 0 1 0
47 1 1 0 -8.16043 -7.5883 0.0 0 1 0
48 1 1 0 -8.29389 -6.77682 0.0 0 1 0
49 1 1 0 -7.43426 -5.95125 0.0 0 1 0
50 1 1 0 -7.57294 -5.43992 0.0 0 1 0
51 1 1 0 -6.57531 -4.66138 0.0 0 1 0
52 1 1 0 -6.13161 -3.66144 0.0 0 1 0
53 1 1 0 -5.13326 -4.12759 0.0 0 1 0
54 1 1 0 -5.02925 -4.84769 0.0 0 1 0
55 1 1 0 -5.20424 -5.80738 0.0 0 1 0
56 1 1 0 -5.9394 -6.61111 0.0 0 1 0
57 1 1 0 -6.92206 -6.23768 0.0 0 1 0
58 1 1 0 -7.36697 -5.95108 0.0 0 1 0
59 1 1 0 -8.35739 -6.7314 0.0 0 1 0
60 1 1 0 -7.69291 -7.53915 0.0 0 1 0
61 1 1 0 -6.69743 7.53385 0.0 0 0 0
62 1 1 0 -7.02856 7.82327 0.0 0 0 0
63 1 1 0 -7.86157 -7.35215 0.0 0 1 0
64 1 1 0 -7.19385 7.66028 0.0 0 0 0
65 1 1 0 -7.60853 7.12961 0.0 0 0 0
66 1 1 0 -6.61444 -7.92379 0.0 0 1 0
67 1 1 0 -5.62004 7.23028 0.0 0 0 0
68 1 1 0 -6.35753 6.50761 0.0 0 0 0
69 1 1 0 -7.18499 6.9785 0.0 0 0 0
70 1 1 0 -7.94877 6.91841 0.0 0 0 0
71 1 1 0 -8.79078 6.08793 0.0 0 0 0
72 1 1 0 -7.89516 5.38758 0.0 0 0 0
73 1 1 0 -6.99769 5.07391 0.0 0 0 0
74 1 1 0 -6.02309 4.1198 0.0 0 0 0
75 1 1 0 -6.948 3.34133 0.0 0 0 0
76 1 1 0 -7.11698 2.37726 0.0 0 0 0
77 1 1 0 -6.31715 1.44401 0.0 0 0 0
78 1 1 0 -5.41635 2.2806 0.0 0 0 0
79 1 1 0 -4.76893 1.61546 0.0 0 0 0
80 1 1 0 -4.12204 0.615684 0.0 0 0 0
81 1 1 0 -4.80521 -0.00660596 0.0 0 0 0
82 1 1 0 -5.6638 0.217738 0.0 0 0 0
83 1 1 0 -6.28311 0.565792 0.0 0 0 0
84 1 1 0 -7.27399 -0.128731 0.0 0 0 0
85 1 1 0 -7.64539 -1.07634 0.0 0 0 0
86 1 1 0 -8.38225 -1.99167 0.0 0 0 0
87 1 1 0 -8.65774 -2.37368 0.0 0 0 0
88 1 1 0 -9.18571 -3.35199 0.0 0 0 0
89 1 1 0 -8.52465 -4.25176 0.0 0 0 0
90 1 1 0 -9.49682 -4.88264 0.0 0 0 0
91 1 1 0 -10.4963 -3.91402 0.0 0 0 0
92 1 1 0 -11.0533 -4.90787 0.0 0 0 0
93 1 1 0 -10.9853 -5.84075 0.0 0 0 0
94 1 1 0 -11.3525 -6.83113 0.0 0 0 0
95 1 1 0 -11.6706 -7.42872 0.0 0 0 0
96 1 1 0 -12.6266 7.58588 0.0 0 -1 0
97 1 1 0 -13.1956 -7.8383 0.0 0 0 0
98 1 1 0 -14.0637 -6.85189 0.0 0 0 0
99 1 1 0 -13.0731 -7.55419 0.0 0 0 0
100 1 1 0 -13.0522 -7.98303 0.0 0 0 0
101 1 1 0 -14.0512 7.07086 0.0 0 -1 0
102 1 1 0 -13.1125 -7.93206 0.0 0 0 0
103 1 1 0 -13.103 -7.61536 0.0 0 0 0
104 1 1 0 -13.1221 7.40558 0.0 0 -1 0
105 1 1 0 -13.048 6.95733 0.0 0 -1 0
106 1 1 0 -12.2167 6.9745 0.0 0 -1 0
107 1 1 0 -11.9053 7.95477 0.0 0 -1 0
108 1 1 0 -12.5017 -7.51313 0.0 0 0 0
109 1 1 0 -11.5613 -7.9361 0.0 0 0 0
110 1 1 0 -12.4435 7.15473 0.0 0 -1 0
111 1 1 0 -13.1987 6.50137 0.0 0 -1 0
112 1 1 0 -12.9751 6.60665 0.0 0 -1 0
113 1 1 0 -12.0824 7.59264 0.0 0 -1 0
114 1 1 0 -11.271 -7.7144 0.0 0 0 0
115 1 1 0 -12.2173 -7.78367 0.0 0 0 0
116 1 1 0 -11.3133 -7.71119 0.0 0 0 0
117 1 1 0 -10.3245 -7.10193 0.0 0 0 0
118 1 1 0 -9.50226 -7.32985 0.0 0 0 0
119 1 1 0 -9.02169 -7.9559 0.0 0 0 0
120 1 1 0 -10.0092 7.19489 0.0 0 -1 0
121 1 1 0 -10.2109 6.7575 0.0 0 -1 0
122 1 1 0 -11.2101 7.38383 0.0 0 -1 0
123 1 1 0 -10.2183 -7.69426 0.0 0 0 0
124 1 1 0 -9.90132 7.5932 0.0 0 -1 0
125 1 1 0 -10.6487 6.59995 0.0 0 -1 0
126 1 1 0 -9.8022 7.5855 0.0 0 -1 0
127 1 1 0 -9.09412 6.59682 0.0 0 -1 0
128 1 1 0 -8.4868 5.81599 0.0 0 -1 0
129 2 2 0 -2.0 8 0 0 0 0
130 3 2 0 -2.0 7 0 0 0 0
131 4 2 0 -2.0 6 0 0 0 0
132 5 2 0 -2.0 5 0 0 0 0
133 6 2 0 -2.0 4 0 0 0 0
134 7 2 0 -2.0 3 0 0 0 0
135 8 2 0 -2.0 -8 0 0 0 0
136 9 2 0 -2.0 -7 0 0 0 0
137 10 2 0 -2.0 -6 0 0 0 0
138 11 2 0 -2.0 -5 0 0 0 0
139 12 2 0 -2.0 -4 0 0 0 0
140 13 2 0 -2.0 -3 0 0 0 0
141 14 2 0 2.0 -8 0 0 0 0
142 15 2 0 2.0 -7 0 0 0 0
143 16 2 0 2.0 -6 0 0 0 0
144 17 2 0 2.0 -5 0 0 0 0
145 18 2 0 2.0 -4 0 0 0 0
146 19 2 0 2.0 -3 0 0 0 0
147 20 2 0 2.0 8 0 0 0 0
148 21 2 0 2.0 7 0 0 0 0
149 22 2 0 2.0 6 0 0 0 0
150 23 2 0 2.0 5 0 0 0 0
151 24 2 0 2.0 4 0 0 0 0
152 25 2 0 2.0 3 0 0 0 0
153 26 3 0 -2 2 0 0 0 0
154 27 3 0 -1 2 0 0 0 0
155 28 3 0 0 2 0 0 0 0
156 29 3 0 1 2 0 0 0 0
157 30 3 0 2 2 0 0 0 0
158 31 3 0 -2 -2 0 0 0 0
159 32 3 0 -1 -2 0 0 0 0
160 33 3 0 0 -2 0 0 0 0
161 34 3 0 1 -2 0 0 0 0
162 35 3 0 2 -2 0 0 0 0
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
61 1 61 62
62 1 62 63
63 1 63 64
64 1 64 65
65 1 65 66
66 1 66 67
67 1 67 68
68 1 68 69
69 1 69 70
70 1 70 71
71 1 71 72
72 1 72 73
73 1 73 74
74 1 74 75
75 1 75 76
76 1 76 77
77 1 77 78
78 1 78 79
79 1 79 80
80 1 80 81
81 1 81 82
82 1 82 83
83 1 83 84
84 1 84 85
85 1 85 86
86 1 86 87
87 1 87 88
88 1 88 89
89 1 89 90
90 1 90 91
91 1 91 92
92 1 92 93
93 1 93 94
94 1 94 95
95 1 95 96
96 1 96 97
97 1 97 98
98 1 98 99
99 1 99 100
100 1 100 101
101 1 101 102
102 1 102 103
103 1 103 104
104 1 104 105
105 1 105 106
106 1 106 107
107 1 107 108
108 1 108 109
109 1 109 110
110 1 110 111
111 1 111 112
112 1 112 113
113 1 113 114
114 1 114 115
115 1 115 116
116 1 116 117
117 1 117 118
118 1 118 119
119 1 119 120
120 1 120 121
121 1 121 122
122 1 122 123
123 1 123 124
124 1 124 125
125 1 125 126
126 1 126 127
127 1 127 128