# 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 # chain_chain_unreacted 50 atoms 51 bonds 84 angles 118 dihedrals 20 impropers Coords 1 24.391510010 0.871569991 -1.658939958 2 25.323530197 1.410570025 -1.658939958 3 23.161520004 1.581570029 -1.658939958 4 23.161520004 3.081569910 -1.658939958 5 21.931529999 0.871569991 -1.658939958 6 20.999530792 1.410570025 -1.658939958 7 21.931529999 -0.548430026 -1.658939958 8 20.999530792 -1.087419987 -1.658939958 9 23.161520004 -1.258419991 -1.658939958 10 23.161520004 -2.335429907 -1.658939958 11 24.391510010 -0.548430026 -1.658939958 12 25.323530197 -1.087419987 -1.658939958 13 24.027519226 3.486569881 -1.301939964 14 21.883520126 3.630569935 -2.220940113 15 21.933509827 4.372580051 -2.319940090 16 21.240520477 2.807569981 -2.514940023 17 28.359209061 3.254519939 -1.372130036 18 27.081209183 3.803519964 -1.934129953 19 27.131210327 4.545519829 -2.033129930 20 26.438219070 2.980520010 -2.228130102 21 13.465809822 0.682529986 -1.658939958 22 14.397820473 1.221529961 -1.658939958 23 12.235819817 1.392529964 -1.658939958 24 12.235819817 2.892529964 -1.658939958 25 11.005820274 0.682529986 -1.658939958 26 10.073820114 1.221529961 -1.658939958 27 11.005820274 -0.737469971 -1.658939958 28 10.073820114 -1.276460052 -1.658939958 29 12.235819817 -1.447460055 -1.658939958 30 12.235819817 -2.524470091 -1.658939958 31 13.465809822 -0.737469971 -1.658939958 32 14.397820473 -1.276460052 -1.658939958 33 13.101819992 3.297529936 -1.301939964 34 10.957819939 3.441529989 -2.220940113 35 18.663520813 0.855480015 -1.372130036 36 19.595510483 1.394479990 -1.372130036 37 17.433509827 1.565479994 -1.372130036 38 17.433509827 3.065479994 -1.372130036 39 16.203510284 0.855480015 -1.372130036 40 15.271510124 1.394479990 -1.372130036 41 16.203510284 -0.564520001 -1.372130036 42 15.271510124 -1.103520036 -1.372130036 43 17.433509827 -1.274520040 -1.372130036 44 17.433509827 -2.351520061 -1.372130036 45 18.663520813 -0.564520001 -1.372130036 46 19.595510483 -1.103520036 -1.372130036 47 18.299509048 3.470479965 -1.015130043 48 16.155509949 3.614480019 -1.934129953 49 16.205509186 4.356480122 -2.033129930 50 15.512510300 2.791480064 -2.228130102 Types 1 cp 2 hc 3 cp 4 c1 5 cp 6 hc 7 cp 8 hc 9 cp 10 hc 11 cp 12 hc 13 hc 14 c2 15 hc 16 hc 17 c1 18 c2 19 hc 20 hc 21 cp 22 hc 23 cp 24 c1 25 cp 26 hc 27 cp 28 hc 29 cp 30 hc 31 cp 32 hc 33 hc 34 c2 35 cp 36 hc 37 cp 38 c1 39 cp 40 hc 41 cp 42 hc 43 cp 44 hc 45 cp 46 hc 47 hc 48 c2 49 hc 50 hc Charges 1 -0.129000 2 0.123700 3 0.026600 4 -0.018200 5 -0.129000 6 0.123700 7 -0.173400 8 0.140300 9 -0.113400 10 0.128800 11 -0.173400 12 0.140300 13 0.051800 14 -0.069600 15 0.035400 16 0.035400 17 -0.018200 18 -0.069600 19 0.035400 20 0.035400 21 -0.129000 22 0.123700 23 0.026600 24 -0.018200 25 -0.129000 26 0.123700 27 -0.173400 28 0.140300 29 -0.113400 30 0.128800 31 -0.173400 32 0.140300 33 0.051800 34 -0.069600 35 -0.129000 36 0.123700 37 0.026600 38 -0.018200 39 -0.129000 40 0.123700 41 -0.173400 42 0.140300 43 -0.113400 44 0.128800 45 -0.173400 46 0.140300 47 0.051800 48 -0.069600 49 0.035400 50 0.035400 Molecules 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 1 11 1 12 1 13 1 14 1 15 1 16 1 17 1 18 1 19 1 20 1 21 1 22 1 23 1 24 1 25 1 26 1 27 1 28 1 29 1 30 1 31 1 32 1 33 1 34 1 35 1 36 1 37 1 38 1 39 1 40 1 41 1 42 1 43 1 44 1 45 1 46 1 47 1 48 1 49 1 50 1 Bonds 1 cp-hc 1 2 2 cp-cp 1 3 3 cp-cp 1 11 4 cp-c1 3 4 5 cp-cp 3 5 6 hc-c1 13 4 7 c1-c2 4 14 8 c1-c2 4 18 9 cp-hc 5 6 10 cp-cp 5 7 11 cp-hc 7 8 12 cp-cp 7 9 13 cp-hc 9 10 14 cp-cp 9 11 15 cp-hc 11 12 16 hc-c2 15 14 17 hc-c2 16 14 18 c1-c2 17 18 19 hc-c2 19 18 20 hc-c2 20 18 21 cp-hc 21 22 22 cp-cp 21 23 23 cp-cp 21 31 24 cp-c1 23 24 25 cp-cp 23 25 26 hc-c1 33 24 27 c1-c2 24 34 28 c1-c2 24 48 29 cp-hc 25 26 30 cp-cp 25 27 31 cp-hc 27 28 32 cp-cp 27 29 33 cp-hc 29 30 34 cp-cp 29 31 35 cp-hc 31 32 36 cp-hc 35 36 37 cp-cp 35 37 38 cp-cp 35 45 39 cp-c1 37 38 40 cp-cp 37 39 41 hc-c1 47 38 42 c1-c2 38 48 43 cp-hc 39 40 44 cp-cp 39 41 45 cp-hc 41 42 46 cp-cp 41 43 47 cp-hc 43 44 48 cp-cp 43 45 49 cp-hc 45 46 50 hc-c2 49 48 51 hc-c2 50 48 Angles 1 cp-cp-hc 3 1 2 2 cp-cp-hc 11 1 2 3 cp-cp-cp 3 1 11 4 cp-cp-c1 1 3 4 5 cp-cp-cp 1 3 5 6 cp-cp-c1 5 3 4 7 cp-c1-hc 3 4 13 8 cp-c1-c2 3 4 14 9 cp-c1-c2 3 4 18 10 hc-c1-c2 13 4 14 11 hc-c1-c2 13 4 18 12 c2-c1-c2 14 4 18 13 cp-cp-hc 3 5 6 14 cp-cp-cp 3 5 7 15 cp-cp-hc 7 5 6 16 cp-cp-hc 5 7 8 17 cp-cp-cp 5 7 9 18 cp-cp-hc 9 7 8 19 cp-cp-hc 7 9 10 20 cp-cp-cp 7 9 11 21 cp-cp-hc 11 9 10 22 cp-cp-cp 1 11 9 23 cp-cp-hc 1 11 12 24 cp-cp-hc 9 11 12 25 hc-c2-c1 15 14 4 26 hc-c2-c1 16 14 4 27 hc-c2-hc 15 14 16 28 c1-c2-c1 4 18 17 29 hc-c2-c1 19 18 4 30 hc-c2-c1 20 18 4 31 hc-c2-c1 19 18 17 32 hc-c2-c1 20 18 17 33 hc-c2-hc 19 18 20 34 cp-cp-hc 23 21 22 35 cp-cp-hc 31 21 22 36 cp-cp-cp 23 21 31 37 cp-cp-c1 21 23 24 38 cp-cp-cp 21 23 25 39 cp-cp-c1 25 23 24 40 cp-c1-hc 23 24 33 41 cp-c1-c2 23 24 34 42 cp-c1-c2 23 24 48 43 hc-c1-c2 33 24 34 44 hc-c1-c2 33 24 48 45 c2-c1-c2 34 24 48 46 cp-cp-hc 23 25 26 47 cp-cp-cp 23 25 27 48 cp-cp-hc 27 25 26 49 cp-cp-hc 25 27 28 50 cp-cp-cp 25 27 29 51 cp-cp-hc 29 27 28 52 cp-cp-hc 27 29 30 53 cp-cp-cp 27 29 31 54 cp-cp-hc 31 29 30 55 cp-cp-cp 21 31 29 56 cp-cp-hc 21 31 32 57 cp-cp-hc 29 31 32 58 cp-cp-hc 37 35 36 59 cp-cp-hc 45 35 36 60 cp-cp-cp 37 35 45 61 cp-cp-c1 35 37 38 62 cp-cp-cp 35 37 39 63 cp-cp-c1 39 37 38 64 cp-c1-hc 37 38 47 65 cp-c1-c2 37 38 48 66 hc-c1-c2 47 38 48 67 cp-cp-hc 37 39 40 68 cp-cp-cp 37 39 41 69 cp-cp-hc 41 39 40 70 cp-cp-hc 39 41 42 71 cp-cp-cp 39 41 43 72 cp-cp-hc 43 41 42 73 cp-cp-hc 41 43 44 74 cp-cp-cp 41 43 45 75 cp-cp-hc 45 43 44 76 cp-cp-cp 35 45 43 77 cp-cp-hc 35 45 46 78 cp-cp-hc 43 45 46 79 c1-c2-c1 24 48 38 80 hc-c2-c1 49 48 24 81 hc-c2-c1 50 48 24 82 hc-c2-c1 49 48 38 83 hc-c2-c1 50 48 38 84 hc-c2-hc 49 48 50 Dihedrals 1 hc-cp-cp-c1 2 1 3 4 2 cp-cp-cp-hc 5 3 1 2 3 cp-cp-cp-c1 11 1 3 4 4 cp-cp-cp-cp 11 1 3 5 5 cp-cp-cp-hc 9 11 1 2 6 hc-cp-cp-hc 2 1 11 12 7 cp-cp-cp-cp 3 1 11 9 8 cp-cp-cp-hc 3 1 11 12 9 cp-cp-c1-hc 1 3 4 13 10 cp-cp-c1-c2 1 3 4 14 11 cp-cp-c1-c2 1 3 4 18 12 cp-cp-c1-hc 5 3 4 13 13 cp-cp-c1-c2 5 3 4 14 14 cp-cp-c1-c2 5 3 4 18 15 cp-cp-cp-hc 1 3 5 6 16 cp-cp-cp-cp 1 3 5 7 17 hc-cp-cp-c1 6 5 3 4 18 cp-cp-cp-c1 7 5 3 4 19 cp-c1-c2-hc 3 4 14 15 20 cp-c1-c2-hc 3 4 14 16 21 hc-c1-c2-hc 13 4 14 15 22 hc-c1-c2-hc 13 4 14 16 23 c2-c1-c2-hc 18 4 14 15 24 c2-c1-c2-hc 18 4 14 16 25 cp-c1-c2-c1 3 4 18 17 26 cp-c1-c2-hc 3 4 18 19 27 cp-c1-c2-hc 3 4 18 20 28 hc-c1-c2-c1 13 4 18 17 29 hc-c1-c2-hc 13 4 18 19 30 hc-c1-c2-hc 13 4 18 20 31 c2-c1-c2-c1 14 4 18 17 32 c2-c1-c2-hc 14 4 18 19 33 c2-c1-c2-hc 14 4 18 20 34 cp-cp-cp-hc 3 5 7 8 35 cp-cp-cp-cp 3 5 7 9 36 hc-cp-cp-hc 6 5 7 8 37 cp-cp-cp-hc 9 7 5 6 38 cp-cp-cp-hc 5 7 9 10 39 cp-cp-cp-cp 5 7 9 11 40 hc-cp-cp-hc 8 7 9 10 41 cp-cp-cp-hc 11 9 7 8 42 cp-cp-cp-cp 7 9 11 1 43 cp-cp-cp-hc 7 9 11 12 44 cp-cp-cp-hc 1 11 9 10 45 hc-cp-cp-hc 10 9 11 12 46 hc-cp-cp-c1 22 21 23 24 47 cp-cp-cp-hc 25 23 21 22 48 cp-cp-cp-c1 31 21 23 24 49 cp-cp-cp-cp 31 21 23 25 50 cp-cp-cp-hc 29 31 21 22 51 hc-cp-cp-hc 22 21 31 32 52 cp-cp-cp-cp 23 21 31 29 53 cp-cp-cp-hc 23 21 31 32 54 cp-cp-c1-hc 21 23 24 33 55 cp-cp-c1-c2 21 23 24 34 56 cp-cp-c1-c2 21 23 24 48 57 cp-cp-c1-hc 25 23 24 33 58 cp-cp-c1-c2 25 23 24 34 59 cp-cp-c1-c2 25 23 24 48 60 cp-cp-cp-hc 21 23 25 26 61 cp-cp-cp-cp 21 23 25 27 62 hc-cp-cp-c1 26 25 23 24 63 cp-cp-cp-c1 27 25 23 24 64 cp-c1-c2-c1 23 24 48 38 65 cp-c1-c2-hc 23 24 48 49 66 cp-c1-c2-hc 23 24 48 50 67 hc-c1-c2-c1 33 24 48 38 68 hc-c1-c2-hc 33 24 48 49 69 hc-c1-c2-hc 33 24 48 50 70 c2-c1-c2-c1 34 24 48 38 71 c2-c1-c2-hc 34 24 48 49 72 c2-c1-c2-hc 34 24 48 50 73 cp-cp-cp-hc 23 25 27 28 74 cp-cp-cp-cp 23 25 27 29 75 hc-cp-cp-hc 26 25 27 28 76 cp-cp-cp-hc 29 27 25 26 77 cp-cp-cp-hc 25 27 29 30 78 cp-cp-cp-cp 25 27 29 31 79 hc-cp-cp-hc 28 27 29 30 80 cp-cp-cp-hc 31 29 27 28 81 cp-cp-cp-cp 27 29 31 21 82 cp-cp-cp-hc 27 29 31 32 83 cp-cp-cp-hc 21 31 29 30 84 hc-cp-cp-hc 30 29 31 32 85 hc-cp-cp-c1 36 35 37 38 86 cp-cp-cp-hc 39 37 35 36 87 cp-cp-cp-c1 45 35 37 38 88 cp-cp-cp-cp 45 35 37 39 89 cp-cp-cp-hc 43 45 35 36 90 hc-cp-cp-hc 36 35 45 46 91 cp-cp-cp-cp 37 35 45 43 92 cp-cp-cp-hc 37 35 45 46 93 cp-cp-c1-hc 35 37 38 47 94 cp-cp-c1-c2 35 37 38 48 95 cp-cp-c1-hc 39 37 38 47 96 cp-cp-c1-c2 39 37 38 48 97 cp-cp-cp-hc 35 37 39 40 98 cp-cp-cp-cp 35 37 39 41 99 hc-cp-cp-c1 40 39 37 38 100 cp-cp-cp-c1 41 39 37 38 101 cp-c1-c2-c1 37 38 48 24 102 cp-c1-c2-hc 37 38 48 49 103 cp-c1-c2-hc 37 38 48 50 104 hc-c1-c2-c1 47 38 48 24 105 hc-c1-c2-hc 47 38 48 49 106 hc-c1-c2-hc 47 38 48 50 107 cp-cp-cp-hc 37 39 41 42 108 cp-cp-cp-cp 37 39 41 43 109 hc-cp-cp-hc 40 39 41 42 110 cp-cp-cp-hc 43 41 39 40 111 cp-cp-cp-hc 39 41 43 44 112 cp-cp-cp-cp 39 41 43 45 113 hc-cp-cp-hc 42 41 43 44 114 cp-cp-cp-hc 45 43 41 42 115 cp-cp-cp-cp 41 43 45 35 116 cp-cp-cp-hc 41 43 45 46 117 cp-cp-cp-hc 35 45 43 44 118 hc-cp-cp-hc 44 43 45 46 Impropers 1 cp-cp-cp-hc 3 1 11 2 2 cp-cp-cp-c1 1 3 5 4 3 cp-cp-cp-hc 3 5 7 6 4 cp-cp-cp-hc 5 7 9 8 5 cp-cp-cp-hc 7 9 11 10 6 cp-cp-cp-hc 1 11 9 12 7 hc-c2-hc-c1 15 14 16 4 8 cp-cp-cp-hc 23 21 31 22 9 cp-cp-cp-c1 21 23 25 24 10 cp-cp-cp-hc 23 25 27 26 11 cp-cp-cp-hc 25 27 29 28 12 cp-cp-cp-hc 27 29 31 30 13 cp-cp-cp-hc 21 31 29 32 14 cp-cp-cp-hc 37 35 45 36 15 cp-cp-cp-c1 35 37 39 38 16 cp-c1-hc-c2 37 38 47 48 17 cp-cp-cp-hc 37 39 41 40 18 cp-cp-cp-hc 39 41 43 42 19 cp-cp-cp-hc 41 43 45 44 20 cp-cp-cp-hc 35 45 43 46