Continuing the discussion from [lammps-users] difficulty using molecule command to add a molecule:
Hello,
I have been trying to resolve an issue similar to that in the link above - with all extra types, bonds, angles, dihedrals added. The molecule I am trying to add has 40 atoms, 40 bonds, 76 angles, and 96 dihedrals. I tried giving different numbers to the extra/special/per/atom, but I am still getting the same error. I would appreciate any pointers on my mistake.
Thank you.
Best wishes,
Jean
Relevant lines in input file:
units real
atom_style full
boundary p p p
bond_style harmonic
angle_style hybrid fourier cosine/periodic harmonic
dihedral_style harmonic
improper_style fourier
pair_style lj/cut 13
pair_modify tail yes mix arithmetic
special_bonds lj 0.0 0.0 0.0
# FRAMEWORK #
box tilt large
read_data data.4a54aa8 extra/atom/types 4 extra/bond/types 3 extra/angle/types 6 extra/dihedral/types 4 extra/special/per/atom 100
# MOLECULE #
molecule ads molecule.txt toff 4 boff 8 aoff 14 doff 4
mass 5 28.0855
mass 6 15.999
mass 7 12.0000
mass 8 1.0000
bond_coeff 9 350.12 1.65817
bond_coeff 10 189.65 1.87355
bond_coeff 11 200.00 1.09349
angle_coeff 15 harmonic 14.14 144.50215
angle_coeff 16 harmonic 94.50 108.5253
angle_coeff 17 harmonic 49.97 108.833
angle_coeff 18 harmonic 99.94 111.0215
angle_coeff 19 harmonic 120.0 110.0926
angle_coeff 20 harmonic 120.0 108.2526
dihedral_coeff 5 0.01 1 3
dihedral_coeff 6 0.225 1 1
dihedral_coeff 7 1.590 -1 3
dihedral_coeff 8 0.01 1 3
pair_coeff 5 5 0 3.385
pair_coeff 6 6 0.1520 2.39
pair_coeff 7 7 0.3776 3.85
pair_coeff 8 8 0.000 2.00
pair_coeff 5 6 0 2.8875
pair_coeff 5 7 0 3.67
pair_coeff 5 8 0 2.8875
pair_coeff 6 7 0.239573 3.120
pair_coeff 6 8 0.00000 3.000
pair_coeff 7 8 0.00000 3.000
set atom * charge 0.0
info system coeffs out append debug.out
create_atoms 0 random 1 123456 NULL mol ads 456789 overlap 1.0 maxtry 100
Molecule file:
all-atom type
40 atoms
40 bonds
76 angles
96 dihedrals
Types
1 1
2 1
3 1
4 1
5 2
6 2
7 2
8 2
9 3
10 3
11 3
12 3
13 3
14 3
15 3
16 3
17 4
18 4
19 4
20 4
21 4
22 4
23 4
24 4
25 4
26 4
27 4
28 4
29 4
30 4
31 4
32 4
33 4
34 4
35 4
36 4
37 4
38 4
39 4
40 4
Molecules
1 40
2 40
3 40
4 40
5 40
6 40
7 40
8 40
9 40
10 40
11 40
12 40
13 40
14 40
15 40
16 40
17 40
18 40
19 40
20 40
21 40
22 40
23 40
24 40
25 40
26 40
27 40
28 40
29 40
30 40
31 40
32 40
33 40
34 40
35 40
36 40
37 40
38 40
39 40
40 40
Coords
1 2.066644457 0.306427621 0.494605648
2 -0.306462995 2.066610897 -0.494566532
3 0.306394227 -2.06657092 -0.494843814
4 -2.066547343 -0.306431706 0.494808748
5 1.189136818 1.355582038 -0.439011105
6 1.355552277 -1.18913268 0.438826828
7 -1.35539259 1.189114221 0.439321785
8 -1.189126263 -1.355384293 -0.439117974
9 2.056309824 0.864721034 2.267730918
10 3.774629618 0.209243144 -0.224876129
11 -0.865094529 2.056119545 -2.26758561
12 -0.209221633 3.774651311 0.22477335
13 0.864750561 -2.05625142 -2.267948203
14 0.209093419 -3.774562307 0.224610868
15 -3.774577799 -0.209039767 -0.224538579
16 -2.056111994 -0.865125584 2.267806697
17 2.530472251 1.844731545 2.375542242
18 1.02977889 0.941795714 2.637360123
19 2.592415094 0.155514688 2.904611074
20 3.731674054 -0.105344518 -1.271089345
21 4.271175418 1.182678544 -0.185039291
22 4.388400462 -0.511025784 0.323207688
23 -0.156022337 2.592193672 -2.904641451
24 -0.942209043 1.029557509 -2.637120214
25 -1.845137903 2.530247355 -2.375251974
26 0.510920157 4.388414449 -0.323486028
27 -1.182686389 4.271151029 0.185079426
28 0.105559441 3.73178356 1.270931953
29 0.941866571 -1.029725717 -2.637583487
30 1.844751587 -2.530441823 -2.375721521
31 0.155551905 -2.592339308 -2.904851542
32 -0.105536947 -3.731609774 1.270811395
33 -0.511180393 -4.388290646 -0.323514461
34 1.182506605 -4.271154728 0.184808675
35 -3.731683123 0.10577302 -1.270686625
36 -4.271149054 -1.182469628 -0.184881024
37 -4.388292353 0.511127097 0.323742568
38 -1.029562194 -0.942287273 2.637365764
39 -2.592176359 -0.156058148 2.904875927
40 -2.530275414 -1.845156769 2.375425452
Bonds
1 1 1 6
2 1 6 3
3 1 3 8
4 1 8 4
5 1 4 7
6 1 7 2
7 1 2 5
8 1 5 1
9 2 1 9
10 2 1 10
11 2 2 11
12 2 2 12
13 2 3 13
14 2 3 14
15 2 4 15
16 2 4 16
17 3 9 17
18 3 9 18
19 3 9 19
20 3 10 20
21 3 10 21
22 3 10 22
23 3 11 23
24 3 11 24
25 3 11 25
26 3 12 26
27 3 12 27
28 3 12 28
29 3 13 29
30 3 13 30
31 3 13 31
32 3 14 32
33 3 14 33
34 3 14 34
35 3 15 35
36 3 15 36
37 3 15 37
38 3 16 38
39 3 16 39
40 3 16 40
Angles
1 1 1 6 3
2 1 3 8 4
3 1 4 7 2
4 1 2 5 1
5 2 5 1 6
6 2 6 3 8
7 2 8 4 7
8 2 7 2 5
9 3 5 1 9
10 3 5 1 10
11 3 5 2 11
12 3 5 2 12
13 3 6 1 9
14 3 6 1 10
15 3 6 3 13
16 3 6 3 14
17 3 7 2 11
18 3 7 2 12
19 3 7 4 15
20 3 7 4 16
21 3 8 3 13
22 3 8 3 14
23 3 8 4 15
24 3 8 4 16
25 4 9 1 10
26 4 11 2 12
27 4 13 3 14
28 4 15 4 16
29 5 17 9 1
30 5 18 9 1
31 5 19 9 1
32 5 20 10 1
33 5 21 10 1
34 5 22 10 1
35 5 23 11 2
36 5 24 11 2
37 5 25 11 2
38 5 26 12 2
39 5 27 12 2
40 5 28 12 2
41 5 29 13 3
42 5 30 13 3
43 5 31 13 3
44 5 32 14 3
45 5 33 14 3
46 5 34 14 3
47 5 35 15 4
48 5 36 15 4
49 5 37 15 4
50 5 38 16 4
51 5 39 16 4
52 5 40 16 4
53 6 17 9 18
54 6 17 9 19
55 6 18 9 19
56 6 20 10 21
57 6 20 10 22
58 6 21 10 22
59 6 23 11 24
60 6 23 11 25
61 6 24 11 25
62 6 26 12 27
63 6 26 12 28
64 6 27 12 28
65 6 29 13 30
66 6 29 13 31
67 6 30 13 31
68 6 32 14 33
69 6 32 14 34
70 6 33 14 34
71 6 35 15 36
72 6 35 15 37
73 6 36 15 37
74 6 38 16 39
75 6 38 16 40
76 6 39 16 40
Dihedrals
1 1 1 5 2 11
2 1 1 5 2 12
3 1 1 6 3 13
4 1 1 6 3 14
5 1 2 5 1 9
6 1 2 5 1 10
7 1 2 7 4 15
8 1 2 7 4 16
9 1 3 6 1 9
10 1 3 6 1 10
11 1 3 8 4 15
12 1 3 8 4 16
13 1 4 7 2 11
14 1 4 7 2 12
15 1 4 8 3 13
16 1 4 8 3 14
17 2 1 5 2 7
18 2 1 6 3 8
19 2 2 5 1 6
20 2 2 7 4 8
21 2 3 6 1 5
22 2 3 8 4 7
23 2 4 7 2 5
24 2 4 8 3 6
25 3 5 1 9 17
26 3 5 1 9 18
27 3 5 1 9 19
28 3 5 1 10 20
29 3 5 1 10 21
30 3 5 1 10 22
31 3 5 2 11 23
32 3 5 2 11 24
33 3 5 2 11 25
34 3 5 2 12 26
35 3 5 2 12 27
36 3 5 2 12 28
37 3 6 1 9 17
38 3 6 1 9 18
39 3 6 1 9 19
40 3 6 1 10 20
41 3 6 1 10 21
42 3 6 1 10 22
43 3 6 3 13 29
44 3 6 3 13 30
45 3 6 3 13 31
46 3 6 3 14 32
47 3 6 3 14 33
48 3 6 3 14 34
49 3 7 2 11 23
50 3 7 2 11 24
51 3 7 2 11 25
52 3 7 2 12 26
53 3 7 2 12 27
54 3 7 2 12 28
55 3 7 4 15 35
56 3 7 4 15 36
57 3 7 4 15 37
58 3 7 4 16 38
59 3 7 4 16 39
60 3 7 4 16 40
61 3 8 3 13 29
62 3 8 3 13 30
63 3 8 3 13 31
64 3 8 3 14 32
65 3 8 3 14 33
66 3 8 3 14 34
67 3 8 4 15 35
68 3 8 4 15 36
69 3 8 4 15 37
70 3 8 4 16 38
71 3 8 4 16 39
72 3 8 4 16 40
73 4 9 1 10 20
74 4 9 1 10 21
75 4 9 1 10 22
76 4 10 1 9 17
77 4 10 1 9 18
78 4 10 1 9 19
79 4 11 2 12 26
80 4 11 2 12 27
81 4 11 2 12 28
82 4 12 2 11 23
83 4 12 2 11 24
84 4 12 2 11 25
85 4 13 3 14 32
86 4 13 3 14 33
87 4 13 3 14 34
88 4 14 3 13 29
89 4 14 3 13 30
90 4 14 3 13 31
91 4 15 4 16 38
92 4 15 4 16 39
93 4 15 4 16 40
94 4 16 4 15 35
95 4 16 4 15 36
96 4 16 4 15 37
Error:
Read molecule template ads:
40 molecules
0 fragments
40 atoms with max type 8
40 bonds with max type 11
76 angles with max type 20
96 dihedrals with max type 8
0 impropers with max type 0
Setting atom values ...
1440 settings made for charge
WARNING: Molecule attributes do not match system attributes (src/molecule.cpp:1696)
ERROR: Molecule topology/atom exceeds system topology/atom (src/molecule.cpp:1724)
Last command: create_atoms 0 random 1 123456 NULL mol ads 456789 overlap 1.0 maxtry 1000