简单量子化学问题答疑专帖

sobereva · 发表于 Post on 2024-5-10 22:56:26

xjun 发表于 2024-5-10 16:02
是的，我是按文献的方法想做想用高斯和antechamber做配体分子RESP电荷计算，然后分子动力学模拟。没接触 ...

你那种做法早过时了
仔细看
RESP拟合静电势电荷的原理以及在Multiwfn中的计算
http://sobereva.com/441（http://bbs.keinsci.com/thread-10880-1-1.html）
计算RESP原子电荷的超级懒人脚本（一行命令就算出结果）
http://sobereva.com/476（http://bbs.keinsci.com/thread-12858-1-1.html）
RESP2原子电荷的思想以及在Multiwfn中的计算
http://sobereva.com/531（http://bbs.keinsci.com/thread-16190-1-1.html）
ORCA结合Multiwfn计算RESP、RESP2和1.2*CM5原子电荷的懒人脚本
http://sobereva.com/637（http://bbs.keinsci.com/thread-28178-1-1.html）

liu19950830 · 发表于 Post on 2024-5-11 17:29:05

我用MCPY.py生成金属蛋白酶的小模型高斯输入文件，通过g16进行优化时总是SCF不收敛。其中尝试了stable=opt可以优化成功，但是再进行opt优化时还是SCF不收敛；也尝试了 SCF=conver=6 IOp(7/127=-99)不行
这是我的初始输入文件最后不收敛求各位大神老师帮忙分析一下附件为输出收敛失败的log文件

%Chk=npt_bdtps_small_opt.chk
%Mem=30000MB
%NProcShared=30
#p B3LYP/6-31G* Geom=PrintInputOrient Integral=(Grid=UltraFine)  Opt

CLR

-1  1
H       63.084 89.469 79.409
C       62.800 88.960 80.330
H       62.715 89.670 81.153
C       63.560 87.640 80.700
C       62.840 86.810 81.820
O       61.690 86.310 81.700
O       63.490 86.540 82.880
H       61.828 88.529 80.090
H       64.460 87.900 81.250
H       63.710 86.990 79.830
H       59.488 89.969 83.944
C       59.720 89.460 84.880
H       59.642 90.094 85.763
C       61.150 88.800 84.710
C       61.650 87.780 85.700
O       61.360 87.870 86.920
O       62.460 86.890 85.310
H       59.042 88.633 85.089
H       61.870 89.600 84.560
H       61.060 88.310 83.740
H       67.464 76.345 85.424
C       67.270 77.360 85.770
H       66.724 77.346 86.713
C       66.540 78.260 84.780
C       66.200 79.620 85.350
N       66.950 80.650 85.040
O       65.280 79.950 86.080
H       68.219 77.869 85.940
H       65.580 77.890 84.410
H       67.120 78.460 83.880
H       67.810 80.560 84.510
H       66.520 81.540 85.230
H       65.147 76.598 87.460
C       64.420 76.650 88.270
H       64.673 75.984 89.095
C       63.020 76.630 87.640
C       62.760 77.850 86.680
O       63.070 79.000 87.080
O       62.050 77.720 85.710
H       64.490 77.604 88.792
H       62.350 76.670 88.500
H       62.860 75.690 87.120
H       67.128 79.166 90.745
C       66.620 80.130 90.760
H       65.708 80.145 91.356
C       66.380 80.540 89.300
O       65.320 79.750 88.710
H       67.358 80.848 91.119
H       67.260 80.420 88.660
H       66.300 81.630 89.320
H       65.740 78.960 88.380
H       62.492 82.971 92.809
C       61.560 83.060 92.250
H       60.669 82.782 92.814
C       61.710 82.300 90.950
C       62.620 82.900 89.910
C       63.050 82.100 88.700
O       64.140 82.330 88.060
O       62.390 81.180 88.190
H       61.352 84.101 92.002
H       60.680 82.160 90.630
H       62.180 81.360 91.230
H       63.530 83.090 90.490
H       62.320 83.890 89.570
Mg       63.720 80.810 86.910
Mg       60.940 84.670 82.030
Mg       64.050 86.160 84.590
P       63.470 82.610 82.240
P       64.250 82.910 84.780
C       64.860 83.880 80.550
O       64.440 82.620 80.990
O       62.630 83.850 82.290
O       63.380 81.880 85.430
C       66.190 84.100 81.230
O       62.580 81.410 82.210
O       65.490 82.950 85.500
C       67.050 85.110 81.080
O       64.580 82.550 83.350
O       63.650 84.300 84.820
C       66.700 86.370 80.340
C       68.420 85.040 81.650
C       69.520 84.600 80.680
C       69.320 83.270 80.070
C       68.990 83.030 78.870
C       69.310 81.600 78.200
C       68.600 84.110 77.980
C       69.640 81.590 76.680
C       69.810 80.140 76.130
C       70.970 79.500 75.950
C       71.050 78.010 75.500
C       72.310 80.070 76.040
H       71.600 77.440 76.260
H       70.050 77.560 75.380
H       71.530 77.960 74.510
H       73.080 79.330 76.320
H       72.580 80.470 75.050
H       72.380 80.950 76.680
H       66.600 87.250 80.990
H       67.520 86.560 79.640
H       65.800 86.260 79.720
H       67.920 84.760 78.550
H       69.460 84.790 77.900
H       68.250 83.960 76.950
H       64.140 84.700 80.650
H       65.000 83.850 79.470
H       68.830 82.040 76.090
H       70.510 82.240 76.540
H       70.450 84.560 81.250
H       69.780 85.380 79.960
H       66.510 83.250 81.840
H       68.910 79.540 76.180
H       68.780 86.060 81.840
H       68.420 84.390 82.530
H       70.180 81.130 78.680
H       68.510 80.880 78.410
H       69.560 82.410 80.700

收敛失败Log输出文件部分内容如下

npt_bdtps_opt1.zip (217.41 KB, 下载次数 Times of downloads: 1)

Cycle 125  Pass 1  IDiag  1:
RMSU=  2.61D-07 CP:  1.00D+00  2.22D+00  1.40D-01  1.46D+00
E= -3909.89538763211    Delta-E=    -0.001021872240 Rises=F Damp=F
DIIS: error= 1.22D-02 at cycle 125 NSaved=  20.
NSaved=20 IEnMin= 6 EnMin= -3910.61722823678    IErMin= 6 ErrMin= 2.17D-03
ErrMax= 1.22D-02  0.00D+00 EMaxC= 1.00D+00 BMatC= 2.59D-01 BMatP= 9.85D-03
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com:  0.102D-01-0.137D+00-0.155D+00-0.975D-01-0.724D+00 0.135D+01
Coeff-Com:  0.173D+01 0.874D+00 0.141D+01 0.566D+01-0.789D+01-0.646D+00
Coeff-Com:  0.183D+01-0.234D+01 0.792D+00 0.180D+01-0.614D+01 0.386D+01
Coeff-Com:  0.213D+01-0.232D+01
Coeff:    0.102D-01-0.137D+00-0.155D+00-0.975D-01-0.724D+00 0.135D+01
Coeff:    0.173D+01 0.874D+00 0.141D+01 0.566D+01-0.789D+01-0.646D+00
Coeff:    0.183D+01-0.234D+01 0.792D+00 0.180D+01-0.614D+01 0.386D+01
Coeff:    0.213D+01-0.232D+01
Gap=    0.057 Goal= None Shift= 0.000
RMSDP=4.39D-06 MaxDP=1.31D-03 DE=-1.02D-03 OVMax= 9.34D-04

Cycle 126  Pass 1  IDiag  1:
RMSU=  1.97D-06 CP:  1.00D+00  3.00D+00  9.19D-01  8.79D-01  1.55D+00
E= -3909.89778674732    Delta-E=    -0.002399115208 Rises=F Damp=F
DIIS: error= 1.22D-02 at cycle 126 NSaved=  20.
NSaved=20 IEnMin= 6 EnMin= -3910.61722823678    IErMin= 6 ErrMin= 2.17D-03
ErrMax= 1.22D-02  0.00D+00 EMaxC= 1.00D+00 BMatC= 2.57D-01 BMatP= 9.85D-03
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com:  0.103D-01-0.137D+00-0.155D+00-0.996D-01-0.735D+00 0.136D+01
Coeff-Com:  0.175D+01 0.909D+00 0.156D+01 0.615D+01-0.850D+01-0.810D+00
Coeff-Com:  0.192D+01-0.229D+01 0.907D+00 0.178D+01-0.702D+01 0.423D+01
Coeff-Com: -0.666D+00 0.830D+00
Coeff:    0.103D-01-0.137D+00-0.155D+00-0.996D-01-0.735D+00 0.136D+01
Coeff:    0.175D+01 0.909D+00 0.156D+01 0.615D+01-0.850D+01-0.810D+00
Coeff:    0.192D+01-0.229D+01 0.907D+00 0.178D+01-0.702D+01 0.423D+01
Coeff:    -0.666D+00 0.830D+00
Gap=    0.057 Goal= None Shift= 0.000
RMSDP=3.31D-06 MaxDP=6.82D-04 DE=-2.40D-03 OVMax= 6.17D-04

Cycle 127  Pass 1  IDiag  1:
RMSU=  1.04D-06 CP:  1.00D+00  2.82D+00  4.18D-01  1.70D+00  3.00D+00
                  CP: -1.22D-01
E= -3909.89633934448    Delta-E=       0.001447402839 Rises=F Damp=F
DIIS: error= 1.22D-02 at cycle 127 NSaved=  20.
NSaved=20 IEnMin= 6 EnMin= -3910.61722823678    IErMin= 6 ErrMin= 2.17D-03
ErrMax= 1.22D-02  0.00D+00 EMaxC= 1.00D+00 BMatC= 2.58D-01 BMatP= 9.85D-03
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com:  0.103D-01-0.138D+00-0.155D+00-0.990D-01-0.734D+00 0.136D+01
Coeff-Com:  0.175D+01 0.912D+00 0.157D+01 0.620D+01-0.855D+01-0.807D+00
Coeff-Com:  0.190D+01-0.227D+01 0.913D+00 0.178D+01-0.701D+01 0.421D+01
Coeff-Com:  0.599D+00-0.440D+00
Coeff:    0.103D-01-0.138D+00-0.155D+00-0.990D-01-0.734D+00 0.136D+01
Coeff:    0.175D+01 0.912D+00 0.157D+01 0.620D+01-0.855D+01-0.807D+00
Coeff:    0.190D+01-0.227D+01 0.913D+00 0.178D+01-0.701D+01 0.421D+01
Coeff:    0.599D+00-0.440D+00
Gap=    0.058 Goal= None Shift= 0.000
RMSDP=1.49D-06 MaxDP=3.39D-04 DE= 1.45D-03 OVMax= 3.69D-04

Cycle 128  Pass 1  IDiag  1:
RMSU=  1.44D-07 CP:  1.00D+00  2.24D+00  6.03D-01  9.94D-01  3.00D+00
                  CP: -1.59D-01  1.28D+00
E= -3909.89576808106    Delta-E=       0.000571263412 Rises=F Damp=F
DIIS: error= 1.22D-02 at cycle 128 NSaved=  20.
NSaved=20 IEnMin= 6 EnMin= -3910.61722823678    IErMin= 6 ErrMin= 2.17D-03
ErrMax= 1.22D-02  0.00D+00 EMaxC= 1.00D+00 BMatC= 2.58D-01 BMatP= 9.85D-03
IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00
Coeff-Com:  0.102D-01-0.137D+00-0.155D+00-0.989D-01-0.725D+00 0.135D+01
Coeff-Com:  0.172D+01 0.863D+00 0.137D+01 0.550D+01-0.769D+01-0.590D+00
Coeff-Com:  0.185D+01-0.243D+01 0.778D+00 0.179D+01-0.606D+01 0.385D+01
Coeff-Com: -0.865D+00 0.655D+00
Coeff:    0.102D-01-0.137D+00-0.155D+00-0.989D-01-0.725D+00 0.135D+01
Coeff:    0.172D+01 0.863D+00 0.137D+01 0.550D+01-0.769D+01-0.590D+00
Coeff:    0.185D+01-0.243D+01 0.778D+00 0.179D+01-0.606D+01 0.385D+01
Coeff:    -0.865D+00 0.655D+00
Gap=    0.056 Goal= None Shift= 0.000
RMSDP=5.69D-06 MaxDP=1.74D-03 DE= 5.71D-04 OVMax= 1.29D-03

>>>>>>>>>> Convergence criterion not met.
SCF Done:  E(RB3LYP) =  -3909.89576808    A.U. after  129 cycles
         NFock=128  Conv=0.57D-05    -V/T= 2.0077
KE= 3.880135291971D+03 PE=-2.886892269970D+04 EE= 1.125828347287D+04
Convergence failure -- run terminated.
Error termination via Lnk1e in /opt/software/g16-A.03/g16/l502.exe at Sat May 11 00:09:52 2024.
Job cpu time:    0 days 23 hours 27 minutes 56.3 seconds.
Elapsed time:    0 days  0 hours 47 minutes  8.7 seconds.
File lengths (MBytes):  RWF= 574 Int=    0 D2E=    0 Chk=    73 Scr=    1

moiumuio · 发表于 Post on 2024-5-11 21:14:52

Hi everyone,
To study intramolecular charge transfer of DMABN like in the figure below. I am going to do in 2 step:
Step 1:
(GS): Optimize at S0 with wB97XD/ma-def2-SVP level
(LE, ICT): Optimize at S1 with td(root=1) wB97XD/ma-def2-SVP level
Step 2:
Calculate fragment charge of each structure have been found on step 1
Am I correct?
Thank you

wzkchem5 · 发表于 Post on 2024-5-11 21:42:52

moiumuio 发表于 2024-5-11 14:14
Hi everyone,
To study intramolecular charge transfer of DMABN like in the figure below. I am going ...

Yes this is a valid, minimalist study of the intramolecular charge transfer. But frequently it's desirable to do even deeper analyses (especially when you are studying a well-studied molecule), so perhaps you may also want to analyze the transition density, do excited state energy decomposition analysis, etc.

moiumuio · 发表于 Post on 2024-5-11 22:39:43

本帖最后由 moiumuio 于 2024-5-12 10:32 编辑

wzkchem5 发表于 2024-5-11 21:42
Yes this is a valid, minimalist study of the intramolecular charge transfer. But frequently it's d ...

Will the IFCT method, like the one described in section 4.1 of this article (http://sobereva.com/433), be able to explain charge transfer within molecules? Or do I need to find out the fragment charge of the relaxed structure? (the Figure below shows my structure)

sobereva · 发表于 Post on 2024-5-12 03:06:02

moiumuio 发表于 2024-5-11 22:39
Will the IFCT method, like the one described in section 4.1 of this article (http://sobereva.com/4 ...

IFCT is only able to provide interfragment charge transfer during vertical excitation/deexcitation.
If you need to study charge transfer for adiabatic excitation, namely ground state and excited state are optimized respectively, then you have to calculate fragment charge for the two states to characterize the excitation.

sobereva · 发表于 Post on 2024-5-12 03:15:22

liu19950830 发表于 2024-5-11 17:29
我用MCPY.py生成金属蛋白酶的小模型高斯输入文件，通过g16进行优化时总是SCF不收敛。其中尝试了stable=opt ...

解决SCF不收敛问题的方法
http://sobereva.com/61

别乱用stable=opt

EwTE_H · 发表于 Post on 2024-5-12 17:42:58

各位老师好，双环[2.2.1]庚烯被H3O+质子化，优化过渡态并计算频率用#opt=(TS, calcfc, noeigen) freq b3lyp/6-311g(d,p) int=fine可行吗？

sobereva · 发表于 Post on 2024-5-12 17:47:42

EwTE_H 发表于 2024-5-12 17:42
各位老师好，双环[2.2.1]庚烯被H3O+质子化，优化过渡态并计算频率用#opt=(TS, calcfc, noeigen) freq b3lyp ...

可以

dalong331 · 发表于 Post on 2024-5-12 20:42:08

各位老师大家好，一般情况下酯化反应的条件是在酸性环境下反应。现在我想知道他是否在常温下反应？我该怎么进行模拟？

dalong331 · 发表于 Post on 2024-5-13 09:51:34

各位老师好，一般来说酯化反应在强酸的环境下发生反应。现在想知道他是否在常温下进行，该如何进行仿真？

bmo · 发表于 Post on 2024-5-13 20:56:49

请教一下大家，我正在几何优化一个二聚体结构，但是改了好几次关键词运行后都显示502，有没有什么好的方法可以解决这个问题

sobereva · 发表于 Post on 2024-5-13 22:08:14

dalong331 发表于 2024-5-12 20:42
各位老师大家好，一般情况下酯化反应的条件是在酸性环境下反应。现在我想知道他是否在常温下反应？我该怎么 ...

pH环境和温度是两个层面的概念，你列举的条件根本没有可比性

sobereva · 发表于 Post on 2024-5-13 22:09:19

解决SCF不收敛问题的方法
http://sobereva.com/61

另外，我不知道你算这个实际目的是什么，本身就是孤立团簇还是要近似模拟周期性体系，如果是后者用CP2K算强百倍

dalong331 · 发表于 Post on 2024-5-14 10:37:07

sobereva 发表于 2024-5-13 22:08
pH环境和温度是两个层面的概念，你列举的条件根本没有可比性

感谢老师的回复，但我并不想模拟PH环境下的反应，我只想模拟在常温下酯化反应是否能正常进行，模拟在常温下这个反应过程。我该用AIMD还是搜索过渡态的方法？

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酯化反应能在常温下进行吗？

酯化反应能在常温下进行吗？

关于解决用高斯优化二聚体502报错的问题

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[综合交流] 简单量子化学问题答疑专帖

Gaussican 设置好参数 最终优化不收敛

酯化反应能在常温下进行吗？

酯化反应能在常温下进行吗？

关于解决用高斯优化二聚体502报错的问题

浏览过的版块

Gaussican 设置好参数最终优化不收敛