求助：在跑molecular dynamics时，出现l402报错，不知道是什么原因，求指导

哇卡卡卡卡卡 · 发表于 Post on 2022-10-2 20:38:32

我现在正在显性溶剂下跑molecular dynamics，首先对初始过渡态进行采样，在运行的时候，出现了402错误，在“Gaussian 常见报错及解决方法；新手求助报错时的注意事项”中没有找到相应的l402错误，具体的错误如下：
Solvent             : Dichloromethane, Eps= 8.930000 Eps(inf)= 2.028346
------------------------------------------------------------------------------
UFF calculation of energy and first derivatives.
------------------------------------------------------------------------------
Atomic radii for non-electrostatic terms: SMD-CDS.
------------------------------------------------------------------------------
Out-of-memory error in routine PCMMM2 (IEnd= 12794095258 MxCore= 2414961310)
Use %mem=12203MW to provide the minimum amount of memory required to complete this step.
Error termination via Lnk1e in /public/software/apps/g16/g16/l402.exe at Sun Oct  2 20:19:57 2022.
Job cpu time:    0 days  0 hours  0 minutes 48.7 seconds.
Elapsed time:    0 days  0 hours  0 minutes  2.9 seconds.
File lengths (MBytes):  RWF= 124 Int=    0 D2E=    0 Chk=    1 Scr=    1
#############################################
exiting function firstpoint.
Sun Oct  2 20:19:59 CST 2022
Error termination in firstreturn = 1

我试过了不是相应的内存错误，脚本中设置的核数和内存为processors 18、memory 36GB
不知道接下来该怎么处理了，请大佬们指教！

sobereva · 发表于 Post on 2022-10-3 06:26:54

UFF（以及任何分子力场）都没法和SMD以及各种基于PCM的溶剂模型结合使用

哇卡卡卡卡卡 · 发表于 Post on 2022-10-3 09:34:28

本帖最后由哇卡卡卡卡卡于 2022-10-3 09:41 编辑

sobereva 发表于 2022-10-3 06:26
UFF（以及任何分子力场）都没法和SMD以及各种基于PCM的溶剂模型结合使用

谢谢sobereva老师，我把smd关键词删了以后，出现了这种错误：End of file in ZSymb.我发现下面的原子个数变少了，在progdyn程序中的gentail脚本是有空格的，不知道为什么会出现End of file in ZSymb这种错误
Symbolic Z-matrix:
Charge =  0 Multiplicity = 1 for low level calculation on real  system.
Charge =  0 Multiplicity = 1 for high  level calculation on model system.
Charge =  0 Multiplicity = 1 for low level calculation on model system.
C                   -1.50702 0.95218  -1.78289
H                   -0.97308 0.94881  -2.72593
C                   -2.7265 0.11932  -1.51482
C                   -1.46514 1.95911  -0.83921
C                   -2.3318 1.62864 0.21883
C                   -2.92146 0.39078  -0.04184
H                   -0.78245 2.799 -0.83703
H                   -2.42482 2.18551 1.14292
H                   -3.76108  -0.00369 0.52063
C                   -0.38056  -0.71915  -0.39808
C                   -1.39516  -0.92451 0.52265
H                   -2.65716  -0.93096  -1.79792
H                   -3.57057 0.56576  -2.06117
H                   -2.02456  -1.80421 0.4426
H                   -0.26768  -1.35225  -1.27161
C                   0.71101 0.19089  -0.03462
O                   0.65616 0.87609 0.97473
C                   1.88667 0.30892  -0.98438
H                   1.65213 1.05641  -1.75051
H                   2.1007 -0.6346 -1.49149
H                   2.76543 0.64729  -0.43429
H                   -1.24065  -0.53648 1.52197
O                   -14.50034 0.33561 8.47698  M
H                   -14.53772  -0.54448 8.94045  M
H                   -14.8092 0.13407 7.55498  M
O                   -12.07644  -0.49087 10.52527  M
H                   -12.32984 0.46766 10.58143  M
H                   -11.46635  -0.62067 11.30367  M
O                   -3.51947 1.09158 12.91469  M
H                   -2.79922 0.93575 12.20569  M
H                   -4.17838 1.66666 12.44274  M
O                   -1.02359 0.75553 5.97537  M
H                   -1.7986 0.14057 5.94709  M
H                   -1.41609 1.65404 5.82546  M
O                   0.12286 1.89463 12.43575  M
H                   -0.15373 1.02356 12.81906  M
H                   -0.22305 1.87875 11.50712  M
O                   -10.22646  -0.6187 13.91887  M
H                   -10.51138  -1.41184 14.48021  M
H                   -10.2419 0.13931 14.56797  M
O                   -2.19303 6.70008 11.81055  M
H                   -2.30549 5.90586 11.22774  M
H                   -1.40573 6.47918 12.37396  M
O                   -10.29584 1.36345 8.68584  M
H                   -11.18473 1.75516 8.45354  M
H                   -9.93612 1.9696 9.39637  M
O                   -3.81143 2.12843 7.42906  M
H                   -4.19087 1.93368 6.52782  M
H                   -3.21021 2.9034 7.28355  M
O                   -2.42394 3.94312 13.82895  M
H                   -3.34106 4.17318 13.48559  M
H                   -1.87116 3.81069 12.99784  M
O                   -6.51017 2.42609 10.64369  M
H                   -7.18152 1.85579 10.18998  M
H                   -5.89081 2.70218 9.91107  M
O                   -13.24558  -3.60839 10.4727  M
H                   -12.52944  -3.37188 9.81915  M
H                   -12.8569  -4.34683 11.02826  M
O                   -6.47256  -0.04381 13.59651  M
H                   -6.4652 0.23323 12.64137  M
H                   -7.45251 0.37619 13.91932  M
O                   -5.43484 5.61868 11.34117  M
H                   -5.79217 5.33363 10.45731  M
H                   -5.19211 4.77186 11.79975  M
O                   -1.52635  -7.97644 12.54427  M
H                   -1.78179  -7.48023 11.69169  M
H                   -1.5452 -7.25013 13.24155  M
O                   -8.46762 5.08328 5.42281  M
H                   -8.77169 4.24232 4.86006  M
H                   -8.67813 5.79628 4.68356  M
O                   -12.83596 1.94422 13.77335  M
H                   -12.48893 1.22357 13.08376  M
H                   -11.97135 2.30438 14.12041  M
O                   -10.19263  -3.83429 8.1014 M
H                   -10.02757  -3.79427 7.09519  M
H                   -9.86627  -2.92836 8.44164  M
O                   -12.21501  -3.47894 4.90579  M
H                   -12.42199  -3.81096 5.82793  M
H                   -12.77702  -2.66211 4.81008  M
O                   -15.22397 1.75604 11.33669  M
H                   -14.27155 2.20699 11.30499  M
H                   -14.92143 0.79472 11.52818  M
O                   -8.56217  -0.59677 10.76641  M
H                   -9.12893  -1.02173 10.06796  M
H                   -8.45265  -1.31571 11.45637  M
O                   -7.86218  -2.95972 14.38188  M
H                   -7.88109  -2.58733 13.43295  M
H                   -6.75023  -2.96669 14.52926  M
O                   -6.26035 3.29384 14.35226  M
H                   -6.5032 2.99791 13.39093  M
H                   -5.50675 2.68697 14.57874  M
O                   -12.41016  -6.34793 7.40487  M
H                   -11.5749  -6.16558 6.82715  M
H                   -12.33402  -5.7445 8.31691  M
O                   -3.48    -2.79431 9.09284  M
H                   -4.3918 -3.01304 9.42968  M
H                   -3.00185  -2.40343 9.90859  M
O                   -3.5311 -1.09245 15.33379  M
H                   -4.25469  -1.72228 15.08208  M
End of file in ZSymb.
Error termination via Lnk1e in /public/software/apps/g16/g16/l101.exe at Mon Oct  3 09:24:18 2022.
Job cpu time:    0 days  0 hours  0 minutes  7.4 seconds.
Elapsed time:    0 days  0 hours  0 minutes  0.4 seconds.
File lengths (MBytes):  RWF=    6 Int=    0 D2E=    0 Chk= 145 Scr=    1
#############################################
exiting function secondpoint.
Mon Oct  3 09:24:18 CST 2022
Error termination in secondreturn = 2

sobereva · 发表于 Post on 2022-10-4 09:27:13

哇卡卡卡卡卡发表于 2022-10-3 09:34
谢谢sobereva老师，我把smd关键词删了以后，出现了这种错误：End of file in ZSymb.我发现下面的原子个 ...

输入文件末尾必须有两个空行，命令行下运行Gaussian的基本常识

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[Gaussian/gview] 求助：在跑molecular dynamics时，出现l402报错，不知道是什么原因，求指导