简单量子化学问题答疑专帖

kimariyb · 发表于 Post on 2024-7-25 13:28:11

卢老师，请问 xtb 中的 alpb 和 gbsa 模型，哪个的精度更好

Roonry · 发表于 Post on 2024-7-25 14:33:35

Roonry 发表于 2024-7-25 09:59
各位老师好我在用IRI方法研究金属和苯环的弱相互作用，如图所示，呈现了一个蓝色的圆环，想问一下这个怎么 ...

yunninghou · 发表于 Post on 2024-7-25 17:24:08

各位老师好，这是我在优化的一个结构，由于结构里有手性要求，所以原子指向不能动，但是一直在报错，之前同样的内存也算过这么大的结构，但是这个却一直在报错

这是我的输入文件
%mem=36GB
%nprocshared=18
#p b3lyp/genecp opt freq EmpiricalDispersion=GD3

Title Card Required

0 1
C                -8.25957300 -1.24469900 0.44058500
C                -6.76006700 -0.50176600 -1.29500800
C                -8.15024100 -0.63080600 -1.92918700
C                -9.07366300 -0.57530700 -0.69431000
H                -8.61497100 -2.24455800 0.70386700
H                -8.24662400 -0.64880400 1.35859800
H                -5.94952100 -0.81870700 -1.95064300
H                -8.33664200 0.17155200 -2.64405800
H                -8.22318900 -1.59821300 -2.43697900
H                -9.28455800 0.46931400 -0.44446700
H             -10.03214900 -1.07630100 -0.85703800
N                -6.89347800 -1.36822000 -0.11094200
C                -6.50393800 0.98207200 -0.91884800
O                -6.83529600 1.88952100 -1.67416500
N                -5.93226200 1.18289900 0.29362800
H                -5.47717100 0.40618800 0.76068000
C                -5.44334300 2.48857500 0.70435300
H                -5.07317000 3.01994800 -0.18292800
C                -4.21944800 2.21800800 1.58677700
O                -3.77246600 1.07912000 1.67709700
N                -3.65696100 3.27888700 2.25031600
H                -3.95130600 4.17890500 1.89017400
C                -2.21421500 3.21773400 2.52127400
H                -1.95686000 4.19251100 2.95131400
C                -1.49924900 3.23050800 1.13331400
O                -2.16544500 3.35068500 0.10598700
N                -0.14367000 3.31246400 1.11914700
H                0.38933300 2.93084000 1.89264700
C                0.53205100 3.47310900 -0.17276700
H                0.04450100 2.78941900 -0.88117500
C                1.95163900 2.91166500 -0.01612400
O                2.08186300 1.74820500 0.37782700
N                3.00795200 3.69453800 -0.34131300
H                2.82084400 4.61369700 -0.71160400
C                4.42130500 3.26067800 -0.33204200
H                5.00365700 4.16393700 -0.52642400
C                4.77108100 2.38078900 -1.56398400
O                5.71495700 2.69680700 -2.27926300
N                3.96577500 1.30839500 -1.79621500
H                3.20911400 1.13159300 -1.14271200
C                4.07891200 0.50038000 -3.00124500
H                5.04257600 0.74665200 -3.45736500
H                3.28051800 0.73286000 -3.71361300
C                3.98131900 -1.00556900 -2.71939500
O                3.16374800 -1.71488900 -3.30325200
N                4.82489200 -1.45305600 -1.75205700
H                5.60581600 -0.84873800 -1.45155300
C                4.78707900 -2.82705000 -1.27721300
H                3.93797500 -3.30815000 -1.76466300
C                4.60984200 -2.84619800 0.25726800
O                5.59438500 -2.93053300 0.99738100
N                3.36717271 -2.89294924 0.71763652
H                3.32037600 -2.83936700 1.79055100
C                2.05977000 -2.61581900 0.14566000
H                2.00929100 -3.22315100 -0.76367300
C                1.02245400 -3.12434700 1.16707200
O                1.28748294 -3.17359566 2.38312148
N                -0.18029264 -3.39471132 0.64987401
H                -0.31718604 -3.31027296 -0.35623503
C                -2.53879300 -3.38189900 0.31834900
O                -2.22301300 -3.45690800 -0.86986600
N                -3.80605400 -3.11281300 0.69401700
H                -4.13423500 -3.13023900 1.65197100
C                -4.78277700 -2.69256800 -0.30811300
H                -4.34177200 -1.88693700 -0.89845700
C                -6.04285700 -2.25984800 0.45524500
O                -6.30610400 -2.81382600 1.52761000
C                -6.54913500 3.32193700 1.36782200
H                -7.37259300 3.43222400 0.65705800
H                -6.19887000 4.32424700 1.63900200
H                -6.92017100 2.82627200 2.27070400
C                0.39248200 4.90358400 -0.72083600
C                0.62375400 4.98387900 -2.23788300
H                1.05519500 5.58991600 -0.17271100
H                -0.62871000 5.23439300 -0.51333900
C                0.58287500 6.41935900 -2.77157600
H                1.58000100 4.51667000 -2.51496900
H                -0.15306600 4.38424300 -2.73140300
C                0.75238700 6.49371700 -4.29049000
H                -0.36612600 6.89879100 -2.50055600
H                1.37706900 7.01230700 -2.29008200
H                1.68485100 5.96945300 -4.57483200
H                -0.06955200 5.94477300 -4.76783200
N                0.68563200 7.88679300 -4.74771800
H                1.50319300 8.39426900 -4.41032200
H                0.73618100 7.91986200 -5.76457600
C                4.83186900 2.71215800 1.05838400
C                6.14983500 1.90673900 1.08376500
H                4.02351600 2.09117200 1.44360400
H                4.89182500 3.57915200 1.72618600
C                5.85209100 0.40472200 1.19069300
H                6.74757200 2.09560200 0.18703400
H                6.75899200 2.20365200 1.94542400
H                5.33379500 0.21036400 2.13493500
H                5.16399100 0.11076200 0.39074700
C                7.50200290 -1.00424921 0.04726565
N                6.86106329 -0.65772953 1.22620222
H                6.51915198 -1.48704853 1.70527946
N                8.42473787 -2.02901942 0.22047172
H                9.04443172 -2.20518604 -0.55869193
H                8.88618759 -2.05556341 1.12134100
N                7.20052144 -0.43271277 -1.07260527
H                7.83587325 -0.69737243 -1.82475417
C                6.06742800 -3.58153400 -1.64614900
H                6.93304100 -3.15689200 -1.13043800
H                6.24351200 -3.49841900 -2.72510800
C                5.95682400 -5.04393800 -1.28650000
O                4.94429800 -5.60461000 -0.92356700
O                7.13754000 -5.68994100 -1.43639000
H                6.97066100 -6.61956900 -1.19019700
C                1.76778700 -1.12174000 -0.20515700
H                2.62579500 -0.80108800 -0.79063100
H                1.80449300 -0.54937600 0.72255800
C                0.46675100 -0.84839100 -0.92926300
C                -0.49862100 -0.01782900 -0.34211100
C                0.14692900 -1.46436500 -2.15054700
C                -1.76607400 0.13520100 -0.89746800
H                -0.25955900 0.49900400 0.57961100
C                -1.12682500 -1.33038800 -2.70878000
H                0.89579400 -2.05787700 -2.66680400
C                -2.10296500 -0.56820800 -2.05589900
H                -2.51556700 0.74374900 -0.40715000
H                -1.37657400 -1.84882000 -3.63101100
O                -3.40041700 -0.47557000 -2.49307400
H                -3.66624100 -1.27341300 -2.99198900
C                -1.43791100 -3.59353500 1.39869200
H                -1.43224900 -4.66615300 1.65124900
C                -5.14728000 -3.87073300 -1.25441800
H                -5.82300100 -4.56140500 -0.73865900
H                -4.21509700 -4.39588600 -1.47861900
C                -5.68504700 -3.41340200 -2.60034200
O                -5.10722400 -2.57688700 -3.29466900
N                -6.83989900 -3.99975300 -3.01581300
H                -7.18194400 -3.78093600 -3.94196300
H                -7.30481000 -4.71843000 -2.48253400
C                -1.87949800 2.13151800 3.61602500
H                -1.73644300 2.67749600 4.55687000
H                -2.77607700 1.52701600 3.74461300
C                -1.64728000 -2.84405500 2.73357900
H                -2.47821000 -3.32398800 3.26245400
H                -0.76470800 -2.97539700 3.35870900
S                -2.11873700 -1.07085500 2.57545100
C                0.66894300 1.54293000 3.72051600
C                1.43914700 0.36318400 3.53330900
C                2.82068100 0.32780900 3.72411600
C                3.44625000 1.51118500 4.11214600
C                2.70734900 2.69520800 4.30580900
C                1.32736100 2.72220500 4.11803700
C                -0.70497400 1.21347400 3.43404100
C                -0.71401400 -0.13840500 3.10307900
H                3.38380100 -0.58828800 3.56894500
H                4.52216000 1.52180700 4.26225600
H                3.22447600 3.60025100 4.61280600
H                0.76583600 3.63966000 4.28204400
N                0.57123500 -0.63922800 3.15800600
H                0.84877500 -1.60263000 2.98448600

-C -H -O -N -P -S -Cl -F -Si -Na -K -B -Li 0
6-31g*
****
-Cu -Pd -I -Cr -Br -Ag -Ni -Au -Ru -Co -Fe -Rh 0
LANL2DZ
****

-Cu -Pd -I -Cr -Br -Ag -Ni -Au -Ru -Co -Fe -Rh 0
LANL2DZ

这是我报错的那部分
Erroneous write. Write -1 instead of 820032.
fd = 4
orig len = 820032 left = 820032
g_write
Error: segmentation violation
rax 0000000000000000, rbx 00000000000c8340, rcx ffffffffffffffff
rdx 000000000000a4cf, rsp 00007ffebd47dcb8, rbp ffffffffffffffff
rsi 000000000000000b, rdi 000000000000a4cf, r8  00002b272203b2c0
r9  0000000000000000, r10 00007ffebd47d720, r11 0000000000000206
r12 00000000000c8340, r13 0000000000000004, r14 00000000000c8340
r15 0000000003252540
  /lib64/libpthread.so.0(+0xf5d0) [0x2b272222b5d0]
  /lib64/libc.so.6(kill+0x7) [0x2b27227704d7]
  /home/room/g09/l1.exe() [0x49be25]
  /home/room/g09/l1.exe() [0x49c42d]
  /home/room/g09/l1.exe() [0x4b4f72]
  /home/room/g09/l1.exe() [0x4a8f5b]
  /home/room/g09/l1.exe() [0x4c6a7b]
  /home/room/g09/l1.exe() [0x40a7d0]
  /home/room/g09/l1.exe() [0x40a231]
  /home/room/g09/l1.exe() [0x403bc1]
  /home/room/g09/l1.exe() [0x40365c]
  /home/room/g09/l1.exe() [0x4035dd]
  /lib64/libc.so.6(__libc_start_main+0xf5) [0x2b272275c3d5]
  /home/room/g09/l1.exe() [0x4034d9]

wzkchem5 · 发表于 Post on 2024-7-25 17:43:19

yunninghou 发表于 2024-7-25 10:24
各位老师好，这是我在优化的一个结构，由于结构里有手性要求，所以原子指向不能动，但是一直在报错，之前同 ...

上传完整输出文件

sobereva · 发表于 Post on 2024-7-25 19:51:24

yunninghou 发表于 2024-7-25 17:24
各位老师好，这是我在优化的一个结构，由于结构里有手性要求，所以原子指向不能动，但是一直在报错，之前同 ...

参考北京科音中级量子化学培训班（http://www.keinsci.com/workshop/KBQC_content.html）的ppt：

sobereva · 发表于 Post on 2024-7-25 19:51:57

kimariyb 发表于 2024-7-25 13:28
卢老师，请问 xtb 中的 alpb 和 gbsa 模型，哪个的精度更好

半斤八两。对于介电常数低的溶剂原理上ALPB更有优势

15670538028 · 发表于 Post on 2024-7-26 16:57:16

wzkchem5 发表于 2024-7-24 16:38
1. 是的。“没有优化到稳定波函数”指的是程序不断提示有instability，还是出现了scf不收敛？后者应该按 ...

多谢您的耐心解答，还有一点迷惑的地方是，我查看了一些之前的文献在算磁性只提到采用guess=mix，并没有提到进行优化到稳定波函数甚至测试波函数稳定性，而我这个算了很多单点都出现波函数不稳定的问题，这是不是和我算的体系有关还是可能其他什么原因呢？顺便请教一下，如果我直接用CP2K软件算单点，结果也会出现波函数不稳定的问题吗？算出来的结果需要自己检查一下波函数吗？

wzkchem5 · 发表于 Post on 2024-7-26 17:02:26

15670538028 发表于 2024-7-26 09:57
多谢您的耐心解答，还有一点迷惑的地方是，我查看了一些之前的文献在算磁性只提到采用guess=mix，并没有 ...

guess=mix只能保证收敛到正确波函数的概率不是0，对于足够简单的体系（例如开壳层单重态）可以收敛到正确的波函数。但是如果你算两个过渡金属反铁磁耦合的体系，而且两个过渡金属都既可能是高自旋又可能是低自旋的话（例如Fe(III)），那guess=mix收敛到正确波函数的概率就要低很多了，甚至可以说低于50%。甚至guess=mix加上测试波函数稳定性，都不能保证收敛到正确的波函数。此时必须用片段初猜的方法，或者手动旋转一些轨道，确保收敛到你想要的波函数

moiumuio · 发表于 Post on 2024-7-27 10:32:09

Hi everyone,
I am studying binding energy and vertical excitation of complexes. Here is my procedure:
1. opt freq b3lyp/6-311G(d,p) em=gd3bj scrf(solvent=thf)
2. (using geom from 1) td cam-b3lyp/6-311+G(d,p) scrf(solvent=thf) guess=read geom=check iop(9/40=3)
3. (using geom from 1) b3lyp/6-311G(d,p) em=gd3bj counterpoise=2
Is this a optimal procedure or I have to change for a better one?
Thank you

wzkchem5 · 发表于 Post on 2024-7-27 15:06:33

moiumuio 发表于 2024-7-27 03:32
Hi everyone,
I am studying binding energy and vertical excitation of complexes. Here is my procedur ...

Without knowing the structures of your complexes, it's impossible to tell. B3LYP or CAM-B3LYP may be suitable for some complexes but completely unsuitable for others

moiumuio · 发表于 Post on 2024-7-27 15:37:48

wzkchem5 发表于 2024-7-27 15:06
Without knowing the structures of your complexes, it's impossible to tell. B3LYP or CAM-B3LYP may ...

Hi teacher,
Sorry for the unclear question. My complexes including conjugated polymers and nitro(-NO2) contained compounds. And I want to study the binding energy and charge transfer between those. Is the above procedure suitable for my tasks?
Thank you

sobereva · 发表于 Post on 2024-7-29 02:40:07

moiumuio 发表于 2024-7-27 15:37
Hi teacher,
Sorry for the unclear question. My complexes including conjugated polymers and nitro( ...

Even using counterpoise correction, 6-311G** is still too small for evaluating interaction energy. Using 6-311+G(2d,p) instead is highly recommended, see Table 1 in J. Phys. Chem. A 2023, 127, 7023−7035 for comparison of different basis sets. In addition, note that solvation effect affects binding capability significantly.

Your level for TDDFT is generally acceptable.

sobereva · 发表于 Post on 2024-7-29 02:41:12

15670538028 发表于 2024-7-26 16:57
多谢您的耐心解答，还有一点迷惑的地方是，我查看了一些之前的文献在算磁性只提到采用guess=mix，并没有 ...

CP2K也可能收敛到不稳定波函数，用OT的时候这种概率比用对角化更高。不过CP2K没有波函数稳定性测试功能。可以尝试不同初猜/自旋态等看是否有可能收敛到能量更低的状态，也可以做TDDFT计算，如果激发能为负是波函数不稳定的充分非必要条件。

xionglvnan · 发表于 Post on 2024-7-29 17:32:43

各位老师们好，请问一下，我用Gaussian09W,优化带四水的二氧化铀，出现L401报错，Defaulting to unpruned grid for atomic number 92.请问一下如何解决，多谢了。

wzkchem5 · 发表于 Post on 2024-7-29 18:38:11

xionglvnan 发表于 2024-7-29 10:32
各位老师们好，请问一下，我用Gaussian09W,优化带四水的二氧化铀，出现L401报错，Defaulting to unpruned g ...

Inaccurate quadrature in CalDSu才是真正的报错信息。在这个论坛一搜就知道怎么解决

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