简单量子化学问题答疑专帖

sobereva · 发表于 Post on 2023-12-6 07:40:23

KSeGaSn 发表于 2023-12-5 17:32
老师们好，请问两个分子的SOCME、ΔEst乃至荧光、ISC速率这些信息，可以在不同的计算水平下进行比较吗？我 ...

如果结果要对不同体系横向对比，泛函尽量统一

sobereva · 发表于 Post on 2023-12-6 07:42:22

JohnYao 发表于 2023-12-5 21:06
老师您好，抱歉打扰了。想请教下老师有关自由基捕获反应速率的问题。研究背景是这样的，在高温下200-300℃ ...

这不属于量子化学问题，应当单独发主贴

JohnYao · 发表于 Post on 2023-12-6 10:52:59

sobereva 发表于 2023-12-6 07:42
这不属于量子化学问题，应当单独发主贴

收到，抱歉老师。

Newbee_Ccc · 发表于 Post on 2023-12-6 16:50:23

本帖最后由 Newbee_Ccc 于 2023-12-6 17:06 编辑

各位老师好！
最近在做一个蛋白质的MD的时候，发现内部存在金属离子，所以想尝试用MCPB.py来处理，按照流程处理后，在用高斯处理的时候发现失败，结果如附件，我也尝试用了下模板提供的文件似乎没问题，想请教下，我的输入文件是哪里出了问题呢？对于高斯纯属小白，如果问题不合适，还请见谅。

sobereva · 发表于 Post on 2023-12-6 17:38:18

Newbee_Ccc 发表于 2023-12-6 16:50
各位老师好！
最近在做一个蛋白质的MD的时候，发现内部存在金属离子，所以想尝试用MCPB.py来处理，按照流 ...

结构荒谬，SCF容易收敛才怪

包括但不限于圈中的地方
做量化计算要有基本结构化学常识

更多信息看
解决SCF不收敛问题的方法
http://sobereva.com/61

Newbee_Ccc · 发表于 Post on 2023-12-6 18:50:37

sobereva 发表于 2023-12-6 17:38
结构荒谬，SCF容易收敛才怪

包括但不限于圈中的地方

感谢老师的回复，我明确了还是自己蛋白质加H的时候出现了问题，再次感谢指导，后续还是得培训班学习下。

kexin · 发表于 Post on 2023-12-7 13:57:49

输入文件：
%chk=INT-SP.chk
%nprocshared=40
%mem=4GB
#p m06 gen pseudo=read temperature=313.15 scrf=(smd,solvent=thf) gfinput

title

0 1
[坐标省略]

C,H,P,B,O 0
6-311++G(d,p)
****
Cu 0
SDD
****

Cu 0
SDD

以下为log末尾信息：No special actions if energy rises.
Fock matrices will be formed incrementally for  20 cycles.

Cycle 1  Pass 1  IDiag  1:
FoFJK:  IHMeth= 1 ICntrl=    0 DoSepK=F KAlg= 0 I1Cent=          0 FoldK=F
IRaf= 720000000 NMat=    1 IRICut=    1 DoRegI=T DoRafI=F ISym2E= 0 IDoP0=0 IntGTp=1.
FoFCou: FMM=T IPFlag=          0 FMFlag=    100000 FMFlg1=       2001
      NFxFlg=          0 DoJE=F BraDBF=F KetDBF=F FulRan=T
      wScrn=  0.000000 ICntrl=       0 IOpCl=  0 I1Cent=          0 NGrid=          0
      NMat0= 1 NMatS0=    1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Symmetry not used in FoFCou.
FMM levels:  10  Number of levels for PrismC: 9
CoulSu:  requested number of processors reduced to:  35 ShMem 1 Linda.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Job cpu time:    0 days  1 hours 43 minutes 50.8 seconds.
Elapsed time:    0 days  0 hours  2 minutes 52.3 seconds.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.
Insufficient memory for a single shell combination in PrsMar called from Prism/PrismC:
LenV=    1084555 MaxCom=       -276
File lengths (MBytes):  RWF= 5599 Int=    0 D2E=    0 Chk=    2 Scr=    1
Error termination via Lnk1e in /opt/soft/gauss/g16c01_avx2/g16/l502.exe at Thu Dec  7 13:44:47 2023.

sobereva · 发表于 Post on 2023-12-7 14:19:17

kexin 发表于 2023-12-7 13:57
输入文件：
%chk=INT-SP.chk
%nprocshared=40

Gaussian的安装方法及运行时的相关问题
http://sobereva.com/439（http://bbs.keinsci.com/thread-10814-1-1.html）
好好看此文了解怎么正确分配内存

kexin · 发表于 Post on 2023-12-7 14:23:43

sobereva 发表于 2023-12-7 14:19
Gaussian的安装方法及运行时的相关问题
http://sobereva.com/439（http://bbs.keinsci.com/thread-10814 ...

好的，谢谢老师的解答

cokie · 发表于 Post on 2023-12-7 20:54:02

给位老师好，我在ORCA 5.0.3的手册中学习Crystal-QMMM方法的使用，在8.13.4最开始提到了要计算整个晶体的电荷，并给出关键字“Conv Charges false ORCAFFFilename "firstjob.convCharges.ORCAFF.prms"” 用于调用，但是在《8.13.4.1 MOL-CRYSTAL-QMMM》一章中的输入文件范例，并没有调用之前已经收敛的电荷，也没有专门计算电荷。在sob老师的博文http://sobereva.com/604里有提到：“背景电荷可以自洽地自动确定”，

所以我的问题是：
1. 电荷计算是否有必要性，如果有，输入文件范例中忽略掉的电荷调用步骤，我是不是应该补充进去呢？
2. 计算电荷我是否按如下关键词写输入文件即可：
!MOL-CRYSTAL-QMMM
%qmmm
  Conv Charges true
  Conv Charges MaxNCycles 30
  Conv Charges ConvThresh 0.01
  Scale FormalCharge MMAtom 1.
end

*xyzfile 0 1 basename.xyz

谢谢各位老师

zqx12 · 发表于 Post on 2023-12-8 15:00:01

本帖最后由 zqx12 于 2023-12-8 15:01 编辑

各位老师好！我优化出来显示的错误是Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on          energy=1.00D-06.
No special actions if energy rises.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
>>>>>>>>>> Convergence criterion not met.
SCF Done:  E(RB3LYP) =  -752.215623967    A.U. after  129 cycles
         NFock=128  Conv=0.44D-03    -V/T= 2.1920
Convergence failure -- run terminated.
Error termination via Lnk1e in /opt/software/gaussian//g16/l502.exe at Thu Dec  7 17:14:08 2023.
Job cpu time:    0 days  3 hours  8 minutes 43.3 seconds.
Elapsed time:    0 days  0 hours 23 minutes 38.7 seconds.
File lengths (MBytes):  RWF=    43 Int=    0 D2E=    0 Chk=    6 Scr=    1
                                                                     8374,2       Bot
图一是优化出来的结构，图二是我画的初始结构，想请各位老师看下是哪里出了问题

zjxitcc · 发表于 Post on 2023-12-8 15:28:09

表面上是SCF不收敛，实际上原因是忘记给N和O元素定义基组。

sobereva · 发表于 Post on 2023-12-8 18:07:50

zqx12 发表于 2023-12-8 15:00
各位老师好！我优化出来显示的错误是Requested convergence on MAX density matrix=1.00D-06.
Requested ...

此外，甭写毫无意义的noraman
好好看
常见的多余的和被滥用的Gaussian关键词
http://sobereva.com/331（http://bbs.keinsci.com/thread-3460-1-1.html）

内存甭给得那么抠，看
Gaussian的安装方法及运行时的相关问题
http://sobereva.com/439（http://bbs.keinsci.com/thread-10814-1-1.html）

lanl2DZ太过时，仔细看
谈谈赝势基组的选用
http://sobereva.com/373（http://bbs.keinsci.com/thread-5625-1-1.html）

当前体系完全没必要写cartesian，纯粹妨碍几何优化收敛

zqx12 · 发表于 Post on 2023-12-8 20:28:01

sobereva 发表于 2023-12-8 18:07
此外，甭写毫无意义的noraman
好好看
常见的多余的和被滥用的Gaussian关键词

好的，谢谢老师，因为我第一次优化的时候出现了103错误，所以加了Cartesian

zqx12 · 发表于 Post on 2023-12-8 20:30:47

zjxitcc 发表于 2023-12-8 15:28
表面上是SCF不收敛，实际上原因是忘记给N和O元素定义基组。

好的谢谢老师，我想问一下为什么优化出来的结构有的键会断裂，有的原子会重叠，是键长的原因吗

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