We want to use oniom method to calculate aqueos water inside nanotube,in which the C atomtype and other parameters of nanotube seems not be defined. I look up previous papers, showing that the L-J parameter between two oxygen atoms as σOO = 0.315 nm and EOO = 0.1521 kcal/mol.Moreover, the L-J parameters between two carbon atoms are σCC = 0.355nm and ECC = 0.293 kJ/mol, the L-J parameters between carbon and oxygen atoms are σCO = 0.335nm and ECO = 0.103184 kcal/mol. However, we only define the carbon atomtype,as follow:
$force_field_params
NumAtomTypes 2
AtomType -1 0 3.55 0.293
Then, how are the L-J parameters between the carbon and oxygen atoms and between the two oxygen atoms determined? And do the water clusters in the nanotubes need to be defined parameters or is the SPC/E model applied?
It is difficult to answer this question without having a an input file. Is it possible for you to construct a small example (maybe not a nanotube)? What force field are you trying to modify?
Hello! I would like to ask you how to calculate ONIOM and frequency at the same time. We found that the nanotubes are not confined and that the vibrational modes only show the vibrations of the nanotubes, rather than water clusters. The specific input file is as follows:
$rem
JOBTYPE = freq
METHOD = pbe0
BASIS = aug-cc-pVDZ
QM_MM_INTERFACE = oniom
FORCE_FIELD = oplsaa
USER_CONNECT = true
MOLDEN_FORMAT = true
GEOM_OPT_DRIVER = OPTIMIZE
$end
$molecule
0 1
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C 3.6971046615 1.1759468034 5.8996700825 -1 2 5 24 0
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C -2.3298953385 3.1349468034 4.4786700825 -1 60 61 79 0
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C -1.2378953385 3.6909468034 15.1356700825 -1 69 50 72 0
C -2.3298953385 3.1349468034 17.2676700825 -1 72 73 91 0
C -1.2378953385 3.6909468034 16.5566700825 -1 70 71 52 0
C -2.3298953385 3.1349468034 18.6886700825 -1 71 74 93 0
C -1.2378953385 3.6909468034 19.3986700825 -1 73 54 76 0
C -2.3298953385 3.1349468034 21.5306700825 -1 76 95 0 0
C -1.2378953385 3.6909468034 20.8196700825 -1 74 75 56 0
C -3.1968953385 2.2679468034 2.3466700825 -1 79 0 0 0
C -3.7528953385 1.1759468034 4.4786700825 -1 79 80 98 0
C -3.1968953385 2.2679468034 3.7676700825 -1 59 77 78 0
C -3.7528953385 1.1759468034 5.8996700825 -1 78 81 100 0
C -3.1968953385 2.2679468034 6.6096700825 -1 61 80 83 0
C -3.7528953385 1.1759468034 8.7416700825 -1 83 84 102 0
C -3.1968953385 2.2679468034 8.0306700825 -1 63 81 82 0
C -3.7528953385 1.1759468034 10.1626700825 -1 82 85 104 0
C -3.1968953385 2.2679468034 10.8726700825 -1 65 84 87 0
C -3.7528953385 1.1759468034 13.0046700825 -1 87 88 106 0
C -3.1968953385 2.2679468034 12.2936700825 -1 85 67 86 0
C -3.7528953385 1.1759468034 14.4256700825 -1 86 89 108 0
C -3.1968953385 2.2679468034 15.1356700825 -1 69 88 91 0
C -3.7528953385 1.1759468034 17.2676700825 -1 91 92 110 0
C -3.1968953385 2.2679468034 16.5566700825 -1 71 89 90 0
C -3.7528953385 1.1759468034 18.6886700825 -1 90 93 112 0
C -3.1968953385 2.2679468034 19.3986700825 -1 73 92 95 0
C -3.7528953385 1.1759468034 21.5306700825 -1 95 114 0 0
C -3.1968953385 2.2679468034 20.8196700825 -1 75 93 94 0
C -3.9448953385 -0.0340531966 2.3466700825 -1 98 0 0 0
C -3.7528953385 -1.2440531966 4.4786700825 -1 98 99 117 0
C -3.9448953385 -0.0340531966 3.7676700825 -1 97 78 96 0
C -3.7528953385 -1.2440531966 5.8996700825 -1 97 100 119 0
C -3.9448953385 -0.0340531966 6.6096700825 -1 99 80 102 0
C -3.7528953385 -1.2440531966 8.7416700825 -1 102 103 121 0
C -3.9448953385 -0.0340531966 8.0306700825 -1 101 82 100 0
C -3.7528953385 -1.2440531966 10.1626700825 -1 101 104 123 0
C -3.9448953385 -0.0340531966 10.8726700825 -1 103 84 106 0
C -3.7528953385 -1.2440531966 13.0046700825 -1 106 107 125 0
C -3.9448953385 -0.0340531966 12.2936700825 -1 105 104 86 0
C -3.7528953385 -1.2440531966 14.4256700825 -1 105 108 127 0
C -3.9448953385 -0.0340531966 15.1356700825 -1 107 88 110 0
C -3.7528953385 -1.2440531966 17.2676700825 -1 110 111 129 0
C -3.9448953385 -0.0340531966 16.5566700825 -1 109 90 108 0
C -3.7528953385 -1.2440531966 18.6886700825 -1 109 112 131 0
C -3.9448953385 -0.0340531966 19.3986700825 -1 111 92 114 0
C -3.7528953385 -1.2440531966 21.5306700825 -1 114 133 0 0
C -3.9448953385 -0.0340531966 20.8196700825 -1 113 94 112 0
C -3.1968953385 -2.3360531966 2.3466700825 -1 117 0 0 0
C -2.3298953385 -3.2030531966 4.4786700825 -1 117 118 136 0
C -3.1968953385 -2.3360531966 3.7676700825 -1 97 115 116 0
C -2.3298953385 -3.2030531966 5.8996700825 -1 116 119 138 0
C -3.1968953385 -2.3360531966 6.6096700825 -1 99 118 121 0
C -2.3298953385 -3.2030531966 8.7416700825 -1 121 122 140 0
C -3.1968953385 -2.3360531966 8.0306700825 -1 101 119 120 0
C -2.3298953385 -3.2030531966 10.1626700825 -1 120 123 142 0
C -3.1968953385 -2.3360531966 10.8726700825 -1 103 122 125 0
C -2.3298953385 -3.2030531966 13.0046700825 -1 125 126 144 0
C -3.1968953385 -2.3360531966 12.2936700825 -1 123 105 124 0
C -2.3298953385 -3.2030531966 14.4256700825 -1 124 127 146 0
C -3.1968953385 -2.3360531966 15.1356700825 -1 107 126 129 0
C -2.3298953385 -3.2030531966 17.2676700825 -1 129 130 148 0
C -3.1968953385 -2.3360531966 16.5566700825 -1 109 127 128 0
C -2.3298953385 -3.2030531966 18.6886700825 -1 128 131 150 0
C -3.1968953385 -2.3360531966 19.3986700825 -1 111 130 133 0
C -2.3298953385 -3.2030531966 21.5306700825 -1 133 152 0 0
C -3.1968953385 -2.3360531966 20.8196700825 -1 113 131 132 0
C -1.2378953385 -3.7590531966 2.3466700825 -1 136 0 0 0
C -0.0278953385 -3.9510531966 4.4786700825 -1 136 137 155 0
C -1.2378953385 -3.7590531966 3.7676700825 -1 116 134 135 0
C -0.0278953385 -3.9510531966 5.8996700825 -1 135 138 157 0
C -1.2378953385 -3.7590531966 6.6096700825 -1 118 137 140 0
C -0.0278953385 -3.9510531966 8.7416700825 -1 140 141 159 0
C -1.2378953385 -3.7590531966 8.0306700825 -1 120 138 139 0
C -0.0278953385 -3.9510531966 10.1626700825 -1 139 142 161 0
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C -0.0278953385 -3.9510531966 13.0046700825 -1 144 145 163 0
C -1.2378953385 -3.7590531966 12.2936700825 -1 142 124 143 0
C -0.0278953385 -3.9510531966 14.4256700825 -1 143 146 165 0
C -1.2378953385 -3.7590531966 15.1356700825 -1 126 145 148 0
C -0.0278953385 -3.9510531966 17.2676700825 -1 148 149 167 0
C -1.2378953385 -3.7590531966 16.5566700825 -1 128 146 147 0
C -0.0278953385 -3.9510531966 18.6886700825 -1 147 150 169 0
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C -0.0278953385 -3.9510531966 21.5306700825 -1 152 171 0 0
C -1.2378953385 -3.7590531966 20.8196700825 -1 132 150 151 0
C 1.1821046615 -3.7590531966 2.3466700825 -1 155 0 0 0
C 2.2741046615 -3.2030531966 4.4786700825 -1 155 156 174 0
C 1.1821046615 -3.7590531966 3.7676700825 -1 135 153 154 0
C 2.2741046615 -3.2030531966 5.8996700825 -1 154 157 176 0
C 1.1821046615 -3.7590531966 6.6096700825 -1 137 156 159 0
C 2.2741046615 -3.2030531966 8.7416700825 -1 159 160 178 0
C 1.1821046615 -3.7590531966 8.0306700825 -1 139 157 158 0
C 2.2741046615 -3.2030531966 10.1626700825 -1 158 161 180 0
C 1.1821046615 -3.7590531966 10.8726700825 -1 141 160 163 0
C 2.2741046615 -3.2030531966 13.0046700825 -1 163 164 182 0
C 1.1821046615 -3.7590531966 12.2936700825 -1 161 143 162 0
C 2.2741046615 -3.2030531966 14.4256700825 -1 162 165 184 0
C 1.1821046615 -3.7590531966 15.1356700825 -1 145 164 167 0
C 2.2741046615 -3.2030531966 17.2676700825 -1 167 168 186 0
C 1.1821046615 -3.7590531966 16.5566700825 -1 147 165 166 0
C 2.2741046615 -3.2030531966 18.6886700825 -1 166 169 188 0
C 1.1821046615 -3.7590531966 19.3986700825 -1 149 168 171 0
C 2.2741046615 -3.2030531966 21.5306700825 -1 171 190 0 0
C 1.1821046615 -3.7590531966 20.8196700825 -1 151 169 170 0
C 3.1411046615 -2.3360531966 2.3466700825 -1 174 0 0 0
C 3.6971046615 -1.2440531966 4.4786700825 -1 3 174 175 0
C 3.1411046615 -2.3360531966 3.7676700825 -1 154 172 173 0
C 3.6971046615 -1.2440531966 5.8996700825 -1 173 5 176 0
C 3.1411046615 -2.3360531966 6.6096700825 -1 156 175 178 0
C 3.6971046615 -1.2440531966 8.7416700825 -1 7 178 179 0
C 3.1411046615 -2.3360531966 8.0306700825 -1 158 176 177 0
C 3.6971046615 -1.2440531966 10.1626700825 -1 177 9 180 0
C 3.1411046615 -2.3360531966 10.8726700825 -1 160 179 182 0
C 3.6971046615 -1.2440531966 13.0046700825 -1 11 182 183 0
C 3.1411046615 -2.3360531966 12.2936700825 -1 180 162 181 0
C 3.6971046615 -1.2440531966 14.4256700825 -1 181 13 184 0
C 3.1411046615 -2.3360531966 15.1356700825 -1 164 183 186 0
C 3.6971046615 -1.2440531966 17.2676700825 -1 15 186 187 0
C 3.1411046615 -2.3360531966 16.5566700825 -1 166 184 185 0
C 3.6971046615 -1.2440531966 18.6886700825 -1 185 17 188 0
C 3.1411046615 -2.3360531966 19.3986700825 -1 168 187 190 0
C 3.6971046615 -1.2440531966 21.5306700825 -1 19 190 0 0
C 3.1411046615 -2.3360531966 20.8196700825 -1 170 188 189 0
O -0.0182943933 -0.0430859761 13.8578421176 -2 192 193 0 0
H 0.4900721544 -0.7891732947 14.1836396762 -3 191 0 0 0
H 0.0263133514 -0.1094770141 12.8921784052 -3 191 0 0 0
O -0.0312980400 -0.0291403502 10.9800266285 -2 195 196 0 0
H -0.9421396244 -0.0565901924 10.6727157455 -3 194 0 0 0
H 0.3134314733 0.8143434176 10.6725735886 -3 194 0 0 0
$end
$opt
FIXED
1 XYZ
2 XYZ
3 XYZ
4 XYZ
5 XYZ
6 XYZ
7 XYZ
8 XYZ
9 XYZ
10 XYZ
11 XYZ
12 XYZ
13 XYZ
14 XYZ
15 XYZ
16 XYZ
17 XYZ
18 XYZ
19 XYZ
20 XYZ
21 XYZ
22 XYZ
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24 XYZ
25 XYZ
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28 XYZ
29 XYZ
30 XYZ
31 XYZ
32 XYZ
33 XYZ
34 XYZ
35 XYZ
36 XYZ
37 XYZ
38 XYZ
39 XYZ
40 XYZ
41 XYZ
42 XYZ
43 XYZ
44 XYZ
45 XYZ
46 XYZ
47 XYZ
48 XYZ
49 XYZ
50 XYZ
51 XYZ
52 XYZ
53 XYZ
54 XYZ
55 XYZ
56 XYZ
57 XYZ
58 XYZ
59 XYZ
60 XYZ
61 XYZ
62 XYZ
63 XYZ
64 XYZ
65 XYZ
66 XYZ
67 XYZ
68 XYZ
69 XYZ
70 XYZ
71 XYZ
72 XYZ
73 XYZ
74 XYZ
75 XYZ
76 XYZ
77 XYZ
78 XYZ
79 XYZ
80 XYZ
81 XYZ
82 XYZ
83 XYZ
84 XYZ
85 XYZ
86 XYZ
87 XYZ
88 XYZ
89 XYZ
90 XYZ
91 XYZ
92 XYZ
93 XYZ
94 XYZ
95 XYZ
96 XYZ
97 XYZ
98 XYZ
99 XYZ
100 XYZ
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102 XYZ
103 XYZ
104 XYZ
105 XYZ
106 XYZ
107 XYZ
108 XYZ
109 XYZ
110 XYZ
111 XYZ
112 XYZ
113 XYZ
114 XYZ
115 XYZ
116 XYZ
117 XYZ
118 XYZ
119 XYZ
120 XYZ
121 XYZ
122 XYZ
123 XYZ
124 XYZ
125 XYZ
126 XYZ
127 XYZ
128 XYZ
129 XYZ
130 XYZ
131 XYZ
132 XYZ
133 XYZ
134 XYZ
135 XYZ
136 XYZ
137 XYZ
138 XYZ
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140 XYZ
141 XYZ
142 XYZ
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146 XYZ
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148 XYZ
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152 XYZ
153 XYZ
154 XYZ
155 XYZ
156 XYZ
157 XYZ
158 XYZ
159 XYZ
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182 XYZ
183 XYZ
184 XYZ
185 XYZ
186 XYZ
187 XYZ
188 XYZ
189 XYZ
190 XYZ
ENDFIXED
$end
$qm_atoms
191 192 193 194 195 196
$end
what is your user-defined FF parameters section for this job?