计算化学公社

标题: 请问这个结构可以用高斯来优化嘛？ [打印本页]

作者
Author: 大王雷 时间: 2020-11-3 16:46
标题: 请问这个结构可以用高斯来优化嘛？
老师好，请问我想优化一下如下图的分子结构，图上每个波浪线代表一下苯环。请问老师这种结构可以用高斯的来优化嘛？优化之后再分析它和小分子的弱相互作用比如RDG之类的，不知道这种是否可行，还请老师指点
(, 下载次数 Times of downloads: 41)

作者
Author: 喵星大佬 时间: 2020-11-3 16:50
本帖最后由喵星大佬于 2020-11-3 16:52 编辑

两百多个原子，当然可以，但是会很慢吧
如果不做振动分析用orca应该会快很多，包括和小分子相互作用的构型
不过需要选择合适的计算级别，否则会很慢
再就是这个分子应该有很多稳定构象，是不是要做个构象搜索啥的

作者
Author: exity 时间: 2020-11-3 17:08
这种结构感觉用XTB(GFN2)后再DFT会稳一些

作者
Author: wzkchem5 时间: 2020-11-3 22:07

exity 发表于 2020-11-3 17:08
这种结构感觉用XTB(GFN2)后再DFT会稳一些

同意，而且我觉得应该加显式溶剂

作者
Author: 喵星大佬 时间: 2020-11-4 11:09

wzkchem5 发表于 2020-11-3 22:07
同意，而且我觉得应该加显式溶剂

那倒是应该看溶剂是什么

作者
Author: 大王雷 时间: 2020-11-4 14:44

喵星大佬发表于 2020-11-4 11:09
那倒是应该看溶剂是什么

溶剂环境是三甲苯：二氧六环：冰乙酸=3：3：1

作者
Author: 喵星大佬 时间: 2020-11-4 14:50

大王雷发表于 2020-11-4 14:44
溶剂环境是三甲苯：二氧六环：冰乙酸=3：3：1

这种感觉用隐式溶剂也没啥问题

作者
Author: 大王雷 时间: 2020-11-4 19:51

喵星大佬发表于 2020-11-4 14:50
这种感觉用隐式溶剂也没啥问题

请问，分析弱相互作用也要加隐式溶剂吗

作者
Author: wzkchem5 时间: 2020-11-4 20:34

喵星大佬发表于 2020-11-4 14:50
这种感觉用隐式溶剂也没啥问题

乙酸不加显式溶剂感觉还是有些不放心。。。

作者
Author: niobium 时间: 2020-11-4 22:17
这体系积分会screening掉很多，稍微好点的机器优化起来压力不大

作者
Author: 大王雷 时间: 2020-11-6 18:27

niobium 发表于 2020-11-4 22:17
这体系积分会screening掉很多，稍微好点的机器优化起来压力不大

这是我的输入文件，麻烦您看对不对
%chk=TpBD-COOH.chk
%mem=6GB
%nprocshared=8
# opt b3lyp/6-31++g(d,p)

Title Card Required

0 2
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C             -22.93581481 1.91340236 -1.46353031
O             -20.05595130 -3.07491783 -1.45880779
O             -20.05518356 1.81814318 -1.46179354
O             -24.29307759 -0.62804880 -1.46143391
N             -20.85271001 2.03222936 0.16261620
H             -16.87987776 -0.91429834 -2.19274171
H             -21.78465521 1.51887391 -2.79163734
O             -18.51778431 2.34828094 -1.43529241
H             -17.94055958 2.67880448 -2.12751044
C             -18.68485443 10.74038272 0.14755576
O             -19.94319231 10.75282502 0.14632139
O             -17.96008014 11.97309662 0.14323615
H             -18.57481733 12.70598824 0.06219253
N             -27.11913170 -0.50915483 -2.72537003
H             -22.13535447 -4.83616101 -0.64693702
H             -26.59335364 -2.04545144 -0.88393366
C             -25.99689321 5.11623257 -0.64291142
C             -24.60173321 5.11623257 -0.64291142
C             -23.90419521 6.32398357 -0.64291142
C             -24.60184921 7.53249257 -0.64411042
C             -25.99667421 7.53241457 -0.64458942
C             -26.69427521 6.32420857 -0.64359342
H             -22.80451521 6.32406357 -0.64227742
H             -24.05164921 8.48463557 -0.64416942
H             -26.54679621 8.48469557 -0.64554242
H             -27.79387921 6.32439157 -0.64377342
N             -23.86716052 3.84292983 -0.64115355
H             -22.64996582 4.54733719 -0.42528060
H             -24.28788594 1.45541277 -0.62672742
O             -26.71183319 3.87778173 -0.64232621
H             -27.63601623 4.04137598 -0.44052774
O                -3.30681232 7.32120234 -3.72038454
H                -3.09523364 7.64114807 -4.60042386
C                -3.47388244 15.71330412 -2.13753637
O                -4.73222032 15.72574643 -2.13877074
O                -2.74910815 16.94601803 -2.14185598
H                -3.17165126 17.56408756 -2.74272816
H                -4.20398807 -9.95655293 0.69042315

1 2 1.0 6 1.0 10 2.0
2 3 1.0 7 2.0
3 4 1.0 12 2.0
4 5 1.0 8 2.0
5 6 1.0 11 2.0
6 9 2.0
7
8
9
10 13 1.0
11 14 1.0 113 1.0
12 15 1.0 110 1.0
13 31 1.0 63 1.0
14 47 1.0 114 1.0
15 21 1.0 62 1.0
16 17 1.5 21 1.5 26 1.0
17 18 1.5 22 1.0
18 19 1.5 23 1.0
19 20 1.5 24 1.0
20 21 1.5 25 1.0
21
22
23
24
25
26 27 1.0
27
28 29 1.5 33 1.5 34 1.0
29 30 1.5 40 1.0
30 31 1.5 262 1.0
31 32 1.5
32 33 1.5 263 1.0
33 41 1.0
34 35 1.5 39 1.5
35 36 1.5 42 1.0
36 37 1.5 265 1.0
37 38 1.5 74 1.0
38 39 1.5 341 1.0
39 43 1.0
40
41
42
43
44 45 1.5 49 1.5 50 1.0
45 46 1.5 56 1.0
46 47 1.5 57 1.0
47 48 1.5
48 49 1.5 337 1.0
49 58 1.0
50 51 1.5 55 1.5
51 52 1.5 59 1.0
52 53 1.5 335 1.0
53 54 1.5 181 1.0
54 55 1.5 60 1.0
55 61 1.0
56
57
58
59
60
61
62
63
64 65 1.0 69 1.0 71 2.0
65 66 1.0 76 2.0
66 67 1.0 70 2.0
67 68 1.0 73 2.0
68 69 1.0 72 2.0
69 77 2.0
70
71
72
73 74 1.0 109 1.0
74 75 1.0
75
76 88 1.0 111 1.0
77 112 1.0 116 1.0
78 79 1.5 83 1.5 84 1.0
79 80 1.5 85 1.0
80 81 1.5 86 1.0
81 82 1.5 87 1.0
82 83 1.5 90 1.0
83 88 1.0
84
85
86
87
88 89 1.0
89
90 91 1.0
91
92 93 1.5 97 1.5 98 1.0
93 94 1.5 104 1.0
94 95 1.5 118 1.0
95 96 1.5 116 1.0
96 97 1.5 119 1.0
97 105 1.0
98 99 1.5 103 1.5
99 100 1.5 106 1.0
100 101 1.5 121 1.0
101 102 1.5 115 1.0
102 103 1.5 107 1.0
103 108 1.0
104
105
106
107
108
109
110
111
112
113
114
115 134 1.0 138 1.0
116 117 1.0
117
118
119 120 1.0
120
121 122 2.0 123 1.0
122
123 124 1.0
124
125 126 1.0 130 1.0 135 2.0
126 127 1.0 133 2.0
127 128 1.0 134 2.0
128 129 1.0 131 2.0
129 130 1.0 136 2.0
130 132 2.0
131
132
133
134 137 1.0
135 149 1.0 151 1.0
136 172 1.0 173 1.0
137
138
139 140 1.5 144 1.5 145 1.0
140 141 1.5 146 1.0
141 142 1.5 152 1.0
142 143 1.5 149 1.0
143 144 1.5 147 1.0
144 148 1.0
145
146
147
148
149 150 1.0
150
151
152 153 1.0
153
154 155 1.5 159 1.5 160 1.0
155 156 1.5 166 1.0
156 157 1.5 167 1.0
157 158 1.5 172 1.0
158 159 1.5 175 1.0
159 168 1.0
160 161 1.5 165 1.5
161 162 1.5 169 1.0
162 163 1.5 177 1.0
163 164 1.5 269 1.0
164 165 1.5 170 1.0
165 171 1.0
166
167
168
169
170
171
172 174 1.0
173
174
175 176 1.0
176
177 178 2.0 179 1.0
178
179 180 1.0
180
181 191 1.0 192 1.0
182 183 1.0 187 1.0 194 2.0
183 184 1.0 190 2.0
184 185 1.0 191 2.0
185 186 1.0 188 2.0
186 187 1.0 195 2.0
187 189 2.0
188
189
190
191 193 1.0
192
193
194 259 1.0 260 1.0
195 207 1.0 206 1.0
196 197 1.5 201 1.5 206 1.0
197 198 1.5 202 1.0
198 199 1.5 203 1.0
199 200 1.5 204 1.0
200 201 1.5 205 1.0
201 209 1.0
202
203
204
205
206 208 1.0
207
208
209 210 1.0
210
211 212 1.0 216 1.0 271 2.0
212 213 1.0 273 2.0
213 214 1.0 272 2.0
214 215 1.0 274 2.0
215 216 1.0 270 2.0
216 275 2.0
217 218 1.5 222 1.5 223 1.0
218 219 1.5 229 1.0
219 220 1.5 230 1.0
220 221 1.5 259 1.0
221 222 1.5 313 1.0
222 231 1.0
223 224 1.5 228 1.5
224 225 1.5 232 1.0
225 226 1.5 311 1.0
226 227 1.5 308 1.0
227 228 1.5 233 1.0
228 234 1.0
229
230
231
232
233
234
235 236 1.5 240 1.5 241 1.0
236 237 1.5 247 1.0
237 238 1.5 248 1.0
238 239 1.5 317 1.0
239 240 1.5 298 1.0
240 249 1.0
241 242 1.5 246 1.5
242 243 1.5 250 1.0
243 244 1.5 296 1.0
244 245 1.5 293 1.0
245 246 1.5 251 1.0
246 252 1.0
247
248
249
250
251
252
253 254 1.0 258 1.0 302 2.0
254 255 1.0 305 2.0
255 256 1.0 303 2.0
256 257 1.0 306 2.0
257 258 1.0 304 2.0
258 307 2.0
259 261 1.0
260
261
262
263 264 1.0
264
265 266 2.0 267 1.0
266
267 268 1.0
268
269 276 1.0 273 1.0
270
271
272
273 277 1.0
274 294 1.0 293 1.0
275 290 1.0 288 1.0
276
277
278 279 1.5 283 1.5 284 1.0
279 280 1.5 285 1.0
280 281 1.5 291 1.0
281 282 1.5 288 1.0
282 283 1.5 286 1.0
283 287 1.0
284
285
286
287
288 289 1.0
289
290
291 292 1.0
292
293 295 1.0
294
295
296 297 1.0
297
298 299 1.0 301 2.0
299 300 1.0
300
301
302 317 1.0 318 1.0
303 308 1.0 309 1.0
304 332 1.0 330 1.0
305
306
307
308 310 1.0
309
310
311 312 1.0
312
313 314 2.0 315 1.0
314
315 316 1.0
316
317 319 1.0
318
319
320 321 1.5 325 1.5 333 1.0
321 322 1.5 330 1.0
322 323 1.5 326 1.0
323 324 1.5 327 1.0
324 325 1.5 328 1.0
325 329 1.0
326
327
328
329
330 331 1.0
331
332
333 334 1.0
334
335 336 1.0
336
337 338 2.0 339 1.0
338
339 340 1.0
340
341

作者
Author: zjxitcc 时间: 2020-11-6 18:56

大王雷发表于 2020-11-6 18:27
这是我的输入文件，麻烦您看对不对
%chk=TpBD-COOH.chk
%mem=6GB

存在诸多问题：
（1）应该上传压缩后的gjf文件，而非直接把内容贴到这里，太长，很多无用信息，读者看着也不方便；
（2）这明显是闭壳层的分子，是单重态，你怎么可能写二重态，应该检查自己的模型是否有漏了氢原子；
（3）对方法和基组的选择没入门，急需恶补博文
《简谈量子化学计算中DFT泛函的选择》http://sobereva.com/272
《谈谈量子化学中基组的选择》http://sobereva.com/336
《谈谈量子化学研究中什么时候用B3LYP泛函优化几何结构是适当的》http://sobereva.com/557
（4）你没写geom=conn，则坐标后也不应写连接关系（但是你却贴了很多行无用的连接关系）
（5）建议使用#p而非#
（6）这体系8核6GB远远不够，如果你是写在这里作为示例也就罢了。离实际计算的要求差得很多。

最后加一句评论：这两年我见过不少前一句还说自己体系“弱相互作用”，后一句光秃秃B3LYP的，这种的计算结果专业审稿人建议直接拒掉。

作者
Author: 大王雷 时间: 2020-11-6 20:01

zjxitcc 发表于 2020-11-6 18:56
存在诸多问题：
（1）应该上传压缩后的gjf文件，而非直接把内容贴到这里，太长，很多无用信息，读者看着 ...

好的，谢谢您

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