# 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