# LAMMPS Molecule File
# Licensed under CC BY 4.0
# A Set of Tutorials for the LAMMPS Simulation Package (LiveCoMS, 2025)
# By Simon Gravelle, Cecilia M. S. Alvares, Jacob R. Gissinger, and Axel Kohlmeyer
# Please cite doi.org/10.33011/livecoms.6.1.3037
# Find more on GitHub: https://github.com/lammpstutorials
# PEG molecule
59 atoms
58 bonds
104 angles
116 dihedrals
Coords
1 -3.0661409 -3.1122069 -1.2331413
2 -3.0905955 -3.1901295 -0.3069935
3 -1.7871211 -3.4628029 0.1677571
4 -1.7892607 -3.9757321 1.1640826
5 -1.4364998 -2.4400568 0.4558979
6 -0.9585523 -4.2486658 -0.9052389
7 -1.5905948 -5.0815649 -1.3120303
8 -0.0526673 -4.7456765 -0.4700128
9 -0.63208 -3.3539891 -2.0115812
10 0.2145577 -4.0010762 -2.9207664
11 -0.3729619 -4.5629487 -3.6922491
12 1.0240761 -4.5117416 -2.3388433
13 0.9711505 -2.8357534 -3.5251923
14 0.3408715 -1.9581318 -3.822669
15 1.6180273 -3.1186311 -4.3940263
16 1.8975644 -2.4613039 -2.5075514
17 3.0585685 -1.8075132 -3.006783
18 2.8443427 -0.8083913 -3.4607034
19 3.6249113 -2.4323449 -3.7466593
20 3.992363 -1.7272376 -1.8733916
21 4.9511518 -1.186389 -2.07637
22 4.254519 -2.795933 -1.6625937
23 3.423965 -1.0901105 -0.7496133
24 3.8947239 -1.659389 0.516987
25 3.9258208 -0.8841055 1.3251652
26 4.9554296 -2.0063238 0.4150401
27 3.0359709 -2.8971462 1.0103722
28 3.8185678 -3.6568248 1.2752906
29 2.4917984 -3.195833 0.0744643
30 2.0725911 -2.848428 2.0760021
31 1.638817 -1.4838974 2.5253139
32 2.5752075 -1.0062795 2.9080422
33 0.9012089 -1.6500344 3.3573053
34 0.8815328 -0.5306711 1.5538689
35 0.5519052 -1.1815579 0.7041188
36 1.6224746 0.2331944 1.1997508
37 -0.2989756 -0.0199954 2.1694908
38 -0.3033598 1.4095408 2.1280825
39 0.0521263 1.761717 1.1273303
40 0.4747811 1.7876458 2.8392599
41 -1.6030958 1.9523106 2.4553161
42 -1.5646386 2.9988577 2.8519616
43 -1.9732467 1.2583804 3.2576206
44 -2.5225735 1.8953969 1.3081864
45 -3.3669469 3.0741107 1.0973018
46 -3.0220368 3.8450892 1.8318384
47 -4.4858675 3.0095129 1.1439484
48 -3.0599689 3.6382723 -0.3005937
49 -3.982976 3.5193791 -0.9249329
50 -2.1988642 3.09917 -0.7700861
51 -2.7010767 5.025878 -0.199455
52 -1.3877664 5.5169363 -0.1698399
53 -0.8882234 5.1431508 -1.0995853
54 -0.935725 4.957068 0.6896982
55 -1.3304483 7.055419 0.0381237
56 -2.0611646 7.6166778 -0.601446
57 -0.3436857 7.3639388 -0.3955144
58 -1.5631742 7.5380082 1.3714558
59 -2.4256234 7.9039402 1.5299768
Types
1 H
2 OAlc
3 CPos
4 HC
5 HC
6 C
7 HC
8 HC
9 OE
10 C
11 HC
12 HC
13 C
14 HC
15 HC
16 OE
17 C
18 HC
19 HC
20 C
21 HC
22 HC
23 OE
24 C
25 HC
26 HC
27 C
28 HC
29 HC
30 OE
31 C
32 HC
33 HC
34 C
35 HC
36 HC
37 OE
38 C
39 HC
40 HC
41 C
42 HC
43 HC
44 OE
45 C
46 HC
47 HC
48 C
49 HC
50 HC
51 OE
52 C
53 HC
54 HC
55 CPos
56 HC
57 HC
58 OAlc
59 H
Charges
1 0.211
2 -0.328
3 -0.019
4 0.093
5 0.093
6 -0.063
7 0.079
8 0.079
9 -0.295
10 -0.021
11 0.084
12 0.084
13 -0.023
14 0.083
15 0.083
16 -0.283
17 -0.023
18 0.083
19 0.083
20 -0.023
21 0.083
22 0.083
23 -0.283
24 -0.023
25 0.082
26 0.082
27 -0.023
28 0.082
29 0.082
30 -0.283
31 -0.023
32 0.082
33 0.082
34 -0.023
35 0.082
36 0.082
37 -0.283
38 -0.023
39 0.082
40 0.083
41 -0.023
42 0.083
43 0.083
44 -0.283
45 -0.023
46 0.083
47 0.083
48 -0.021
49 0.084
50 0.084
51 -0.295
52 -0.063
53 0.079
54 0.079
55 -0.019
56 0.093
57 0.093
58 -0.328
59 0.211
Bonds
1 g18 13 16
2 g18 16 17
3 g18 20 23
4 g18 23 24
5 g18 27 30
6 g18 30 31
7 g18 34 37
8 g18 37 38
9 g18 41 44
10 g18 44 45
11 g18 48 51
12 g18 51 52
13 g18 6 9
14 g18 9 10
15 g26 17 20
16 g26 24 27
17 g26 31 34
18 g26 38 41
19 g27 10 13
20 g27 3 6
21 g27 45 48
22 g27 52 55
23 g4 10 11
24 g4 10 12
25 g4 13 14
26 g4 13 15
27 g4 17 18
28 g4 17 19
29 g4 20 21
30 g4 20 22
31 g4 24 25
32 g4 24 26
33 g4 27 28
34 g4 27 29
35 g4 3 4
36 g4 3 5
37 g4 31 32
38 g4 31 33
39 g4 34 35
40 g4 34 36
41 g4 38 39
42 g4 38 40
43 g4 41 42
44 g4 41 43
45 g4 45 46
46 g4 45 47
47 g4 48 49
48 g4 48 50
49 g4 52 53
50 g4 52 54
51 g4 55 56
52 g4 55 57
53 g4 6 7
54 g4 6 8
55 g56 2 3
56 g56 55 58
57 g71 1 2
58 g71 58 59
Angles
1 g102 14 13 16
2 g102 15 13 16
3 g102 2 3 4
4 g102 2 3 5
5 g102 21 20 23
6 g102 22 20 23
7 g102 23 24 25
8 g102 23 24 26
9 g102 30 31 32
10 g102 30 31 33
11 g102 35 34 37
12 g102 36 34 37
13 g102 37 38 39
14 g102 37 38 40
15 g102 4 3 5
16 g102 4 3 6
17 g102 44 45 46
18 g102 44 45 47
19 g102 5 3 6
20 g102 52 55 56
21 g102 52 55 57
22 g102 56 55 57
23 g102 56 55 58
24 g102 57 55 58
25 g12 1 2 3
26 g12 13 16 17
27 g12 20 23 24
28 g12 27 30 31
29 g12 34 37 38
30 g12 41 44 45
31 g12 48 51 52
32 g12 55 58 59
33 g12 6 9 10
34 g13 10 13 16
35 g13 16 17 20
36 g13 17 20 23
37 g13 23 24 27
38 g13 3 6 9
39 g13 30 31 34
40 g13 31 34 37
41 g13 37 38 41
42 g13 38 41 44
43 g13 44 45 48
44 g13 45 48 51
45 g13 51 52 55
46 g13 9 10 13
47 g14 11 10 12
48 g14 14 13 15
49 g14 18 17 19
50 g14 21 20 22
51 g14 25 24 26
52 g14 28 27 29
53 g14 32 31 33
54 g14 35 34 36
55 g14 39 38 40
56 g14 42 41 43
57 g14 46 45 47
58 g14 49 48 50
59 g14 51 52 53
60 g14 51 52 54
61 g14 53 52 54
62 g14 7 6 8
63 g14 7 6 9
64 g14 8 6 9
65 g15 2 3 6
66 g15 3 6 7
67 g15 3 6 8
68 g15 52 55 58
69 g15 53 52 55
70 g15 54 52 55
71 g51 10 13 14
72 g51 10 13 15
73 g51 11 10 13
74 g51 12 10 13
75 g51 16 17 18
76 g51 16 17 19
77 g51 17 20 21
78 g51 17 20 22
79 g51 18 17 20
80 g51 19 17 20
81 g51 24 27 28
82 g51 24 27 29
83 g51 25 24 27
84 g51 26 24 27
85 g51 28 27 30
86 g51 29 27 30
87 g51 31 34 35
88 g51 31 34 36
89 g51 32 31 34
90 g51 33 31 34
91 g51 38 41 42
92 g51 38 41 43
93 g51 39 38 41
94 g51 40 38 41
95 g51 42 41 44
96 g51 43 41 44
97 g51 45 48 49
98 g51 45 48 50
99 g51 46 45 48
100 g51 47 45 48
101 g56 49 48 51
102 g56 50 48 51
103 g56 9 10 11
104 g56 9 10 12
Dihedrals
1 g23 1 2 3 6
2 g23 10 13 16 17
3 g23 13 16 17 20
4 g23 17 20 23 24
5 g23 20 23 24 27
6 g23 27 30 31 34
7 g23 3 6 9 10
8 g23 31 34 37 38
9 g23 34 37 38 41
10 g23 38 41 44 45
11 g23 41 44 45 48
12 g23 45 48 51 52
13 g23 48 51 52 55
14 g23 52 55 58 59
15 g23 6 9 10 13
16 g34 2 3 6 9
17 g34 51 52 55 58
18 g46 16 17 20 23
19 g46 30 31 34 37
20 g46 37 38 41 44
21 g46 44 45 48 51
22 g46 9 10 13 16
23 glj14 1 2 3 4
24 glj14 1 2 3 5
25 glj14 11 10 13 14
26 glj14 11 10 13 15
27 glj14 11 10 13 16
28 glj14 12 10 13 14
29 glj14 12 10 13 15
30 glj14 12 10 13 16
31 glj14 13 16 17 18
32 glj14 13 16 17 19
33 glj14 14 13 16 17
34 glj14 15 13 16 17
35 glj14 16 17 20 21
36 glj14 16 17 20 22
37 glj14 18 17 20 21
38 glj14 18 17 20 22
39 glj14 18 17 20 23
40 glj14 19 17 20 21
41 glj14 19 17 20 22
42 glj14 19 17 20 23
43 glj14 2 3 6 7
44 glj14 2 3 6 8
45 glj14 20 23 24 25
46 glj14 20 23 24 26
47 glj14 21 20 23 24
48 glj14 22 20 23 24
49 glj14 23 24 27 28
50 glj14 23 24 27 29
51 glj14 25 24 27 28
52 glj14 25 24 27 29
53 glj14 26 24 27 28
54 glj14 26 24 27 29
55 glj14 27 30 31 32
56 glj14 27 30 31 33
57 glj14 28 27 30 31
58 glj14 29 27 30 31
59 glj14 30 31 34 35
60 glj14 30 31 34 36
61 glj14 32 31 34 35
62 glj14 32 31 34 36
63 glj14 32 31 34 37
64 glj14 33 31 34 35
65 glj14 33 31 34 36
66 glj14 33 31 34 37
67 glj14 34 37 38 39
68 glj14 34 37 38 40
69 glj14 35 34 37 38
70 glj14 36 34 37 38
71 glj14 37 38 41 42
72 glj14 37 38 41 43
73 glj14 39 38 41 42
74 glj14 39 38 41 43
75 glj14 39 38 41 44
76 glj14 4 3 6 7
77 glj14 4 3 6 8
78 glj14 4 3 6 9
79 glj14 40 38 41 42
80 glj14 40 38 41 43
81 glj14 40 38 41 44
82 glj14 41 44 45 46
83 glj14 41 44 45 47
84 glj14 42 41 44 45
85 glj14 43 41 44 45
86 glj14 44 45 48 49
87 glj14 44 45 48 50
88 glj14 46 45 48 49
89 glj14 46 45 48 50
90 glj14 46 45 48 51
91 glj14 47 45 48 49
92 glj14 47 45 48 50
93 glj14 47 45 48 51
94 glj14 48 51 52 53
95 glj14 48 51 52 54
96 glj14 49 48 51 52
97 glj14 5 3 6 7
98 glj14 5 3 6 8
99 glj14 5 3 6 9
100 glj14 50 48 51 52
101 glj14 51 52 55 56
102 glj14 51 52 55 57
103 glj14 53 52 55 56
104 glj14 53 52 55 57
105 glj14 53 52 55 58
106 glj14 54 52 55 56
107 glj14 54 52 55 57
108 glj14 54 52 55 58
109 glj14 56 55 58 59
110 glj14 57 55 58 59
111 glj14 6 9 10 11
112 glj14 6 9 10 12
113 glj14 7 6 9 10
114 glj14 8 6 9 10
115 glj14 9 10 13 14
116 glj14 9 10 13 15