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标题: 求助一个机构优化，总是报错，找不到问题所在，谢谢 [打印本页]

作者
Author: avatar_man 时间: 2021-12-21 12:14
标题: 求助一个机构优化，总是报错，找不到问题所在，谢谢
用pm6优化一个结构，总是报错，不知道为什么。
以下是输入文件，
%chk=Co6_pm6.chk
%mem=64GB
%nprocshared=12
# opt pm6

Co6

0 2
Co             10.46280000 15.35940000 14.06930000
O                11.79990000 16.42520000 13.20130000
O                7.32480000 9.57930000 11.43680000
N                9.96460000 14.39900000 12.38360000
C                9.26380000 13.14470000 12.23070000
C                7.89310000 10.79230000 11.72510000
C                9.27570000 10.83800000 11.56660000
H                9.74340000 10.05860000 11.29040000
C                10.93200000 16.19870000 10.98920000
C                12.15780000 10.73280000 11.78070000
C                7.15470000 14.37400000 12.83170000
H                7.76440000 14.84680000 13.46790000
C                10.90910000 16.63850000 9.64340000
H                10.34410000 16.19500000 9.02160000
C                11.76370000 16.82490000 11.95080000
C                9.97770000 12.01110000 11.80790000
C                7.01010000 15.29630000 11.63000000
C                7.88270000 13.09850000 12.42600000
C                7.19380000 11.90930000 12.15880000
H                6.25180000 11.86730000 12.27410000
C                12.59850000 17.90510000 11.50250000
C                11.68050000 17.68620000 9.21420000
C                5.86190000 14.13090000 13.59630000
C                12.51330000 18.28740000 10.17750000
H                13.05880000 19.01190000 9.89450000
C                10.16020000 15.01840000 11.25180000
H                9.73170000 14.63390000 10.49610000
C                11.48840000 12.08770000 11.56040000
H                11.86360000 12.71170000 12.24600000
C                11.80890000 12.68590000 10.19460000
C                10.96920000 12.51100000 9.10560000
H                10.16400000 12.01790000 9.21060000
C                11.70600000 18.18870000 7.76440000
C                13.58200000 18.57330000 12.46840000
C                12.71360000 9.98720000 10.74460000
H                12.72640000 10.34060000 9.86280000
C                7.42480000 16.62060000 11.73470000
H                7.75390000 16.94590000 12.56430000
C                6.51960000 14.83980000 10.41120000
H                6.22260000 13.94140000 10.32680000
C                12.18580000 10.20150000 13.07000000
H                11.82890000 10.70560000 13.79170000
C                11.28750000 13.04590000 7.86170000
H                10.70320000 12.91780000 7.12370000
C                4.69170000 14.82850000 13.35230000
H                4.65900000 15.45330000 12.63740000
C                13.24900000 8.20280000 12.27010000
H                13.60380000 7.33670000 12.43210000
C                14.58580000 17.51950000 12.96900000
H                14.10040000 16.78330000 13.39660000
H                15.19400000 17.93030000 13.61840000
H                15.10190000 17.17390000 12.21110000
C                5.88240000 13.23210000 14.66600000
H                6.67990000 12.75350000 14.85930000
C                7.36290000 17.46990000 10.64050000
H                7.64690000 18.37260000 10.72420000
C                4.76330000 13.02860000 15.44560000
H                4.79460000 12.41090000 16.16670000
C                12.98100000 13.41480000 10.01880000
H                13.56790000 13.54730000 10.75390000
C                12.72670000 8.94820000 13.31360000
H                12.73900000 8.60060000 14.19770000
C                3.59400000 13.72190000 15.18050000
H                2.81980000 13.57540000 15.71140000
C                13.25070000 8.72670000 10.99280000
H                13.62140000 8.22310000 10.27760000
C                3.56170000 14.62630000 14.14050000
H                2.76610000 15.11330000 13.96110000
C                11.16400000 19.62060000 7.70660000
H                10.21970000 19.62310000 7.96850000
H                11.25070000 19.96600000 6.79350000
H                11.67500000 20.18820000 8.32050000
C                6.46270000 15.69340000 9.31740000
H                6.12930000 15.37640000 8.48620000
C                6.89100000 17.00750000 9.43410000
H                6.85860000 17.58730000 8.68220000
C                12.82510000 19.21700000 13.64000000
H                12.26660000 19.94940000 13.30530000
H                13.46830000 19.56790000 14.29090000
H                12.25780000 18.54440000 14.07140000
C                13.14760000 18.16250000 7.24320000
H                13.69530000 18.78410000 7.76660000
H                13.15910000 18.43090000 6.30080000
H                13.50960000 17.25600000 7.32930000
C                13.29970000 13.95030000 8.77790000
H                14.10220000 14.44670000 8.66880000
C                12.45680000 13.76430000 7.70470000
H                12.67960000 14.12970000 6.85660000
C                5.91710000 9.45900000 11.57470000
H                5.47450000 10.08130000 10.96050000
H                5.65990000 9.67090000 12.49620000
H                5.64540000 8.54170000 11.36230000
C                14.40040000 19.68100000 11.78830000
H                14.89400000 19.30410000 11.03040000
H                15.03240000 20.06250000 12.43280000
H                13.79650000 20.38350000 11.46820000
C                10.85330000 17.31750000 6.84850000
H                11.17390000 16.39230000 6.88620000
H                10.91900000 17.64890000 5.92860000
H                9.91900000 17.35190000 7.14210000
O                9.12570000 16.42520000 14.93720000
O                13.60080000 9.57930000 16.70170000
N                10.96100000 14.39900000 15.75490000
C                11.66180000 13.14470000 15.90780000
C                13.03250000 10.79230000 16.41340000
C                11.64990000 10.83800000 16.57190000
H                11.18220000 10.05860000 16.84810000
C                9.99360000 16.19870000 17.14930000
C                8.76780000 10.73280000 16.35780000
C                13.77090000 14.37400000 15.30680000
H                13.16120000 14.84680000 14.67060000
C                10.01650000 16.63850000 18.49510000
H                10.58150000 16.19500000 19.11690000
C                9.16190000 16.82490000 16.18770000
C                10.94790000 12.01110000 16.33060000
C                13.91550000 15.29630000 16.50850000
C                13.04290000 13.09850000 15.71250000
C                13.73180000 11.90930000 15.97970000
H                14.67380000 11.86730000 15.86440000
C                8.32710000 17.90510000 16.63600000
C                9.24510000 17.68620000 18.92430000
C                15.06370000 14.13090000 14.54220000
C                8.41230000 18.28740000 17.96100000
H                7.86680000 19.01190000 18.24400000
C                10.76540000 15.01840000 16.88670000
H                11.19390000 14.63390000 17.64240000
C                9.43720000 12.08770000 16.57810000
H                9.06200000 12.71170000 15.89250000
C                9.11670000 12.68590000 17.94390000
C                9.95640000 12.51100000 19.03290000
H                10.76160000 12.01790000 18.92790000
C                9.21960000 18.18870000 20.37410000
C                7.34360000 18.57330000 15.67010000
C                8.21200000 9.98720000 17.39390000
H                8.19920000 10.34060000 18.27570000
C                13.50080000 16.62060000 16.40380000
H                13.17170000 16.94590000 15.57420000
C                14.40600000 14.83980000 17.72730000
H                14.70300000 13.94140000 17.81170000
C                8.73980000 10.20150000 15.06850000
H                9.09670000 10.70560000 14.34680000
C                9.63810000 13.04590000 20.27680000
H                10.22240000 12.91780000 21.01480000
C                16.23390000 14.82850000 14.78620000
H                16.26660000 15.45330000 15.50110000
C                7.67660000 8.20280000 15.86840000
H                7.32180000 7.33670000 15.70640000
C                6.33980000 17.51950000 15.16950000
H                6.82520000 16.78330000 14.74190000
H                5.73160000 17.93030000 14.52010000
H                5.82370000 17.17390000 15.92740000
C                15.04320000 13.23210000 13.47250000
H                14.24570000 12.75350000 13.27920000
C                13.56270000 17.46990000 17.49800000
H                13.27870000 18.37260000 17.41430000
C                16.16230000 13.02860000 12.69290000
H                16.13100000 12.41090000 11.97180000
C                7.94460000 13.41480000 18.11970000
H                7.35770000 13.54730000 17.38460000
C                8.19890000 8.94820000 14.82490000
H                8.18660000 8.60060000 13.94080000
C                17.33160000 13.72190000 12.95800000
H                18.10580000 13.57540000 12.42710000
C                7.67490000 8.72670000 17.14570000
H                7.30420000 8.22310000 17.86090000
C                17.36390000 14.62630000 13.99800000
H                18.15950000 15.11330000 14.17740000
C                9.76160000 19.62060000 20.43190000
H                10.70590000 19.62310000 20.17000000
H                9.67490000 19.96600000 21.34500000
H                9.25060000 20.18820000 19.81800000
C                14.46290000 15.69340000 18.82110000
H                14.79630000 15.37640000 19.65230000
C                14.03460000 17.00750000 18.70440000
H                14.06700000 17.58730000 19.45630000
C                8.10050000 19.21700000 14.49850000
H                8.65900000 19.94940000 14.83320000
H                7.45730000 19.56790000 13.84760000
H                8.66780000 18.54440000 14.06710000
C                7.77800000 18.16250000 20.89530000
H                7.23030000 18.78410000 20.37190000
H                7.76650000 18.43090000 21.83770000
H                7.41600000 17.25600000 20.80920000
C                7.62590000 13.95030000 19.36060000
H                6.82340000 14.44670000 19.46970000
C                8.46880000 13.76430000 20.43380000
H                8.24600000 14.12970000 21.28190000
C                15.00850000 9.45900000 16.56380000
H                15.45110000 10.08130000 17.17800000
H                15.26570000 9.67090000 15.64230000
H                15.28020000 8.54170000 16.77620000
C                6.52520000 19.68100000 16.35020000
H                6.03160000 19.30410000 17.10810000
H                5.89320000 20.06250000 15.70570000
H                7.12910000 20.38350000 16.67030000
C                10.07230000 17.31750000 21.29000000
H                9.75170000 16.39230000 21.25230000
H                10.00660000 17.64890000 22.20990000
H                11.00660000 17.35190000 20.99640000

作者
Author: snljty 时间: 2021-12-21 12:53
后面写着很清楚了，自洽场不收敛。看卢老师博文《解决SCF不收敛问题的方法》http://sobereva.com/61。
此体系完全不适用PM6。用PM7或者PM6D3等带色散校正的方法都会好一些。xtb的GFN2大概率会更好。
200个原子，有个主流的服务器直接拿DFT优化没问题，不需要用半经验。

作者
Author: avatar_man 时间: 2021-12-21 14:22
收到，谢谢！我试一下dft，因为原子比较多，原本想着先用pm6预优化下，然后再用dft，这样节省时间。

作者
Author: sobereva 时间: 2021-12-21 18:30

avatar_man 发表于 2021-12-21 14:22
收到，谢谢！我试一下dft，因为原子比较多，原本想着先用pm6预优化下，然后再用dft，这样节省时间。

带过渡金属的体系通常不建议用半经验方法优化，要用半经验层面的就用GFN-xTB，对过渡金属体系远比半经验方法可靠得多
看下文文末PM7和GFN-xTB的对比
将Gaussian与Grimme的xtb程序联用搜索过渡态、产生IRC、做振动分析
http://sobereva.com/421（http://bbs.keinsci.com/thread-10106-1-1.html）

作者
Author: avatar_man 时间: 2021-12-21 19:15

snljty 发表于 2021-12-21 12:53
后面写着很清楚了，自洽场不收敛。看卢老师博文《解决SCF不收敛问题的方法》http://sobereva.com/61。
此 ...

刚才用B3LYP/6-31G*也跑了一遍，一样的报错，还是不能收敛

作者
Author: avatar_man 时间: 2021-12-21 19:15

sobereva 发表于 2021-12-21 18:30
带过渡金属的体系通常不建议用半经验方法优化，要用半经验层面的就用GFN-xTB，对过渡金属体系远比半经验 ...

好的，我再试试，

作者
Author: snljty 时间: 2021-12-21 20:25

avatar_man 发表于 2021-12-21 19:15
刚才用B3LYP/6-31G*也跑了一遍，一样的报错，还是不能收敛

上面给你的博文链接认真看。另外B3LYP也不是很适合过渡金属。

作者
Author: avatar_man 时间: 2021-12-22 08:26

snljty 发表于 2021-12-21 20:25
上面给你的博文链接认真看。另外B3LYP也不是很适合过渡金属。

好的，谢谢啦！

作者
Author: avatar_man 时间: 2021-12-22 21:14
本帖最后由 avatar_man 于 2021-12-22 21:30 编辑

snljty 发表于 2021-12-21 20:25
上面给你的博文链接认真看。另外B3LYP也不是很适合过渡金属。

你好，谢谢，按照sob老师和您的建议，用xtb优化了，也收敛了，

请问之后得到的结构能作为初猜继续用dft进行优化和单点计算吗？会不会还是不收敛？我需要对比类似的其他的结构。谢谢

作者
Author: avatar_man 时间: 2021-12-22 21:40

snljty 发表于 2021-12-21 20:25
上面给你的博文链接认真看。另外B3LYP也不是很适合过渡金属。

另外，还有一个问题，按照sob老师的帖子，安装xtb之后，编辑~/.bashrc，发现之前高斯文件也在这个里面，我直接在这个文件后面加上sob老师让写的语句之后，gaussian运行不了了，请问我哪里是操作错误了吗？谢谢

作者
Author: snljty 时间: 2021-12-22 21:48

avatar_man 发表于 2021-12-22 21:40
另外，还有一个问题，按照sob老师的帖子，安装xtb之后，编辑~/.bashrc，发现之前高斯文件也在这个里面， ...

SCF不收敛就看上面博文去解决SCF不收敛的问题，都跟你提到三次了。.bashrc不要把所有配置都写在一起，很容易冲突。最简单(但绝不是最方便)的方式是把所有的都注释掉，用哪个去掉哪个注释，然后重新登录，用完了再注释掉，再重新登录。稍微方便一些的方法是写一堆shell脚本，用哪个source哪个，然后下次重新退出再登录。最方便的方法是用Environment Modules。如果不知道.bashrc是做什么的，建议先学一天Linux基础。

作者
Author: avatar_man 时间: 2021-12-23 08:41

snljty 发表于 2021-12-22 21:48
SCF不收敛就看上面博文去解决SCF不收敛的问题，都跟你提到三次了。.bashrc不要把所有配置都写在一起，很 ...

按照那篇博文的也正在排除，还没排除完。。。

关于bashrc，我用最简单的吧，现在刚学习，还搞不定复杂的。。。多谢了！

作者
Author: 喵星大佬 时间: 2021-12-23 12:25

snljty 发表于 2021-12-22 21:48
SCF不收敛就看上面博文去解决SCF不收敛的问题，都跟你提到三次了。.bashrc不要把所有配置都写在一起，很 ...

讲道理第二个方法更好用

作者
Author: snljty 时间: 2021-12-23 12:46

喵星大佬发表于 2021-12-23 12:25
讲道理第二个方法更好用

这不是要unload一部分就比较麻烦嘛

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