求助对于配合物如何设置周期性边界条件(PBC)

bomsaude · 发表于 Post on 2015-1-29 00:09:30

本帖最后由 bomsaude 于 2015-1-29 00:25 编辑

有CIF文件，想用MOPAC优化不是单个分子的配合物，在创建输入文件时遇到了PBC的问题，在MOPAC的网上手册中说可以设置PBC，但没有找到具体的操作步骤，例如，对于下面这样的配合物该如何创建输入文件呢？

从WEBCSD上随便下载一个含Co的CIF文件（见附件），结构如下面所示，分子式，空间群和晶胞参数为：

(C12 H10 Co N2 O6)n

Space Group: C 2/c

a 11.373(2) b 7.8632(16) c 13.162(3)

α 90 β 100.92(3) γ 90

用gaussview打开后，存成的gjf文件为：

# pbepbe/3-21g/auto
Title Card Required
0 1
Co -0.62334640 5.53097488 3.23091775
O 10.58432340 4.00000984 1.78592210
O 1.09108089 2.87242696 2.23437348
O 8.67979181 5.43189856 3.66347302
H 8.13040833 5.72126432 3.16629940
H 8.63754862 4.63063848 3.80343638
N 10.22893009 7.17910160 2.04581712
C 10.56013941 0.53391128 2.50370278
C 10.57241405 1.63554560 1.64427866
C 10.04621937 1.47670896 0.36315516
H 7.49838226 2.20720024 12.71430754
C 7.11387337 0.23589600 12.86809922
H 6.71855704 0.12502488 12.03452244
C 9.76959929 7.03520504 0.79480577
H 9.55499251 6.18283416 0.49239187
C -0.11785634 2.94555472 1.93131340
C -0.43383220 0.53391128 3.95813272
N -0.10262288 7.17910160 4.41601838
C 0.35670792 7.03520504 5.66702974
C 0.51904825 0.23589600 6.51740729
C 0.08008784 1.47670896 6.09868035
C -0.44610684 1.63554560 4.81755684
C 10.24416355 2.94555472 4.53052211
O -0.45801619 4.00000984 4.67591341
O 9.03522632 2.87242696 4.22746202
H 0.13453936 2.20720024 6.67119897
H 0.91436458 0.12502488 7.35098407
H 0.57131470 6.18283416 5.96944364
O 1.44651540 5.43189856 2.79836248
H 1.99589888 5.72126432 3.29553611
H 1.48875859 4.63063848 2.65839913
Co -1.87003919 2.33222512 9.69275326
Co 5.06315360 1.59937488 3.23091775
Co 3.81646081 6.26382512 9.69275326
O -1.70470898 3.86319016 11.13774891
O 9.33763060 3.86319016 8.24775760
O 4.89782340 0.06840984 1.78592210
O 5.22848381 0.06840984 4.67591341
O 3.98179102 7.79479016 11.13774891
O 3.65113060 7.79479016 8.24775760
O 7.78853353 4.99077304 10.68929753
O -0.15561191 4.99077304 8.69620898
O 6.77758089 6.80402696 2.23437348
O 3.34872632 6.80402696 4.22746202
O 2.10203353 1.05917304 10.68929753
O 5.53088809 1.05917304 8.69620898
O 0.19982261 2.43130144 9.26019799
O 7.43309902 2.43130144 10.12530852
O 2.99329181 1.50029856 3.66347302
O 7.13301540 1.50029856 2.79836248
O 5.88632261 6.36290144 9.26019799
O 1.74659902 6.36290144 10.12530852
H 0.74920608 2.14193568 9.75737161
H 6.88371554 2.14193568 9.62813490
H 2.44390833 1.78966432 3.16629940
H 7.68239888 1.78966432 3.29553611
H 6.43570608 6.07353568 9.75737161
H 1.19721554 6.07353568 9.62813490
H 0.24206579 3.23256152 9.12023463
H 7.39085583 3.23256152 10.26527188
H 2.95104862 0.69903848 3.80343638
H 7.17525859 0.69903848 2.65839913
H 5.92856579 7.16416152 9.12023463
H 1.70435583 7.16416152 10.26527188
N -1.34931568 0.68409840 10.87785389
N 8.98223730 0.68409840 8.50765262
N 4.54243009 3.24750160 2.04581712
N 5.58387712 3.24750160 4.41601838
N 4.33718432 4.61569840 10.87785389
N 3.29573730 4.61569840 8.50765262
C -1.68052500 7.32928872 10.41996822
C 9.31344662 7.32928872 8.96553829
C 4.87363941 4.46551128 2.50370278
C 5.25266780 4.46551128 3.95813272
C 4.00597500 3.39768872 10.41996822
C 3.62694662 3.39768872 8.96553829
C -1.69279964 6.22765440 11.27939235
C 9.32572126 6.22765440 8.10611417
C 4.88591405 5.56714560 1.64427866
C 5.24039316 5.56714560 4.81755684
C 3.99370036 2.29605440 11.27939235
C 3.63922126 2.29605440 8.10611417
C -1.16660495 6.38649104 12.56051585
C 8.79952657 6.38649104 6.82499066
C 4.35971937 5.40830896 0.36315516
C 5.76658784 5.40830896 6.09868035
C 4.51989505 2.45489104 12.56051585
C 3.11302657 2.45489104 6.82499066
H 1.38123215 5.65599976 0.20936347
H 8.74507505 5.65599976 6.25247203
H 1.81188226 6.13880024 12.71430754
H 5.82103936 6.13880024 6.67119897
H 7.06773215 1.72439976 0.20936347
H 3.05857505 1.72439976 6.25247203
C 1.76574104 7.62730400 0.05557179
C 8.36056617 7.62730400 6.40626372
C 1.42737337 4.16749600 12.86809922
C 6.20554825 4.16749600 6.51740729
C 7.45224104 3.69570400 0.05557179
C 2.67406617 3.69570400 6.40626372
H 2.16105737 7.73817512 0.88914857
H 7.96524984 7.73817512 5.57268694
H 1.03205704 4.05662488 12.03452244
H 6.60086458 4.05662488 7.35098407
H 7.84755737 3.80657512 0.88914857
H 2.27874984 3.80657512 5.57268694
C -0.88998487 0.82799496 12.12886524
C 8.52290649 0.82799496 7.25664127
C 4.08309929 3.10360504 0.79480577
C 6.04320792 3.10360504 5.66702974
C 4.79651513 4.75959496 12.12886524
C 2.83640649 4.75959496 7.25664127
H -0.67537809 1.68036584 12.43127914
H 8.30829972 1.68036584 6.95422737
H 3.86849251 2.25123416 0.49239187
H 6.25781470 2.25123416 5.96944364
H 5.01112191 5.61196584 12.43127914
H 2.62179972 5.61196584 6.95422737
C 8.99747076 4.91764528 10.99235761
C -1.36454913 4.91764528 8.39314890
C 5.56864366 6.87715472 1.93131340
C 4.55766355 6.87715472 4.53052211
C 3.31097076 0.98604528 10.99235761
C 4.32195087 0.98604528 8.39314890
Tv 11.37300000 0.00000000 0.00000000
Tv 0.00000000 7.86320000 0.00000000
Tv -2.49338558 0.00000000 12.92367101

复制代码

这样的坐标加上半经验法的关键词，似乎算不动啊，速度非常慢

请教该如何设置这类配合物的PBC，然后用于MOPAC的半经验方法计算，或者该看看那些相关教程来设置非单个分子配合物的PBC，谢谢了！

AHIKIL.cif (4.13 KB, 下载次数 Times of downloads: 1)

sobereva · 发表于 Post on 2015-1-29 00:44:00

可以看看http://openmopac.net/manual/index.html里面examples当中Solid State Calculations这部分的介绍和例子

bomsaude · 发表于 Post on 2015-1-29 01:27:11

sobereva 发表于 2015-1-29 00:44
可以看看http://openmopac.net/manual/index.html里面examples当中Solid State Calculations这部分的介绍和 ...

谢谢您！我这就把有关固体计算的那部分例子仔细看一看。

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[MOPAC] 求助对于配合物如何设置周期性边界条件(PBC)

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