From owner-chemistry@ccl.net Thu Aug 22 01:45:01 2019 From: "Igors Mihailovs igorsm++cfi.lu.lv" To: CCL Subject: CCL:G: Oniom calculation Message-Id: <-53819-190822014335-22380-LsIH1fyhEAZQHOwO/iPUmg_-_server.ccl.net> X-Original-From: Igors Mihailovs Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="----880OCRJMCT3D9ZMZGWH2G6VC5S3JUD" Date: Thu, 22 Aug 2019 08:43:23 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm * cfi.lu.lv] ------880OCRJMCT3D9ZMZGWH2G6VC5S3JUD Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Nikiwe, This means that linear search faoled, so You can try to avoid it by not us= ing YQC, but, for example, XQC=2E Another possible solution is to rise the = SCF=3D(MaxNR=3DX) option value to suppress calling the linear search (defau= lt is 2, You may try 1 or 0)=2E Also, You can try adding IOp(5/6=3D2123) (w= hich should try to avoid SD/SSD (steepest descent/scaled steepest descent),= but I am not sure anymore what the first "2" meant and why it appeared in = my notes)=2E Regarding the ONIOM spheres=2E=2E=2E Shouldn't You probably be including a= t least those Ag atoms directly connected to the mercapto acid in the high = level of calculation? Best regards, Igors Mihailovs ISSP ULatvia 21 =D0=B0=D0=B2=D0=B3=D1=83=D1=81=D1=82=D0=B0 2019 =D0=B3=2E 17:02:56 GMT+= 03:00, "Nikiwe Mhlanga mhlanga=2Enikiwe,gmail=2Ecom" =D0=BF=D0=B8=D1=88=D0=B5=D1=82: >Dear CCL subscribers, > >We are using Gaussian16 to optimize and calculate frequency for a large >metal >system (4mercaptobenzoic acid chemisorbed on a silver cluster) using >ONIOM >(QM/MM)=2E we are treating the high layer, mercaptobenzoic acid with QM >and >low layer (Ag) with MM level of theory=2E > > > >our input file > >%chk=3DAg38_MBA1=2Echk >%mem =3D 5GB >%lindaworkers=3Dcnode0657=2Ecm=2Ecluster,cnode0906=2Ecm=2Ecluster >#p opt=3D(calcfc,tight) freq=3Draman oniom(pbepbe/lanl2dz:uff) >geom=3Dconnectivity int=3Dultrafine >scf=3D(maxcycle=3D550,yqc,novaracc,vshift,fermi) > >Chemisorption of 4-MBA via the S-end on Ag38 > >0 2 0 1 0 1 > Ag- 0 -0=2E087538 3=2E780638 -2=2E135173 L > Ag- 0 0=2E615213 -4=2E386287 -0=2E456889 L > Ag- 0 2=2E829965 -3=2E263123 1=2E265124 L H-H_ = 49 > Ag- 0 3=2E976204 -1=2E855176 -1=2E155020 L > Ag- 0 1=2E665691 -2=2E899508 -2=2E881852 L > Ag- 0 -0=2E598942 -1=2E649918 4=2E200849 L > Ag- 0 2=2E333531 -2=2E041848 3=2E419830 L > Ag- 0 2=2E789235 0=2E944243 3=2E494113 L > Ag- 0 -2=2E511342 -2=2E594676 2=2E814294 L > Ag- 0 -1=2E806843 -4=2E057143 0=2E230665 L > Ag- 0 0=2E168591 -3=2E740375 2=2E355867 L > Ag- 0 -2=2E215108 -1=2E722228 0=2E605513 L > Ag- 0 0=2E819420 -0=2E269238 2=2E851871 L > Ag- 0 1=2E680469 -2=2E235243 -0=2E577234 L > Ag- 0 4=2E283287 -0=2E732592 1=2E589185 L H-H_ = 49 > Ag- 0 2=2E291430 1=2E736077 -0=2E334834 L > Ag- 0 3=2E746658 2=2E194141 1=2E517127 L H-H_ = 49 > Ag- 0 4=2E316879 0=2E645926 -1=2E013672 L > Ag- 0 -3=2E610548 -2=2E155021 -1=2E294531 L > Ag- 0 -1=2E191423 -3=2E274241 -2=2E498385 L > Ag- 0 -2=2E731567 -0=2E932626 -3=2E350923 L > Ag- 0 -0=2E775108 0=2E272067 -2=2E677735 L > Ag- 0 0=2E181427 -1=2E311149 -4=2E203277 L > Ag- 0 2=2E763581 -0=2E242360 -3=2E306407 L > Ag- 0 0=2E675001 1=2E666398 -3=2E983753 L > Ag- 0 2=2E569425 2=2E593788 -2=2E565890 L > Ag- 0 -0=2E079166 1=2E336138 4=2E402200 L > Ag- 0 -4=2E249702 -0=2E625375 1=2E241064 L > Ag- 0 -2=2E677469 0=2E262864 3=2E531853 L > Ag- 0 -3=2E842229 1=2E876387 1=2E383742 L > Ag- 0 -1=2E565519 2=2E916640 3=2E080574 L > Ag- 0 -1=2E573313 2=2E331846 0=2E753050 L > Ag- 0 1=2E286577 3=2E308372 2=2E708779 L > Ag- 0 -0=2E527428 4=2E483001 0=2E690975 L > Ag- 0 1=2E880836 4=2E076154 -0=2E015485 L > Ag- 0 -4=2E041769 0=2E734748 -1=2E324399 L > Ag- 0 -2=2E765623 3=2E335672 -1=2E063434 L > Ag- 0 -2=2E232937 2=2E088889 -3=2E215876 L > H-H_ 0 7=2E812188 1=2E301680 1=2E865590 H > C-C_3 0 7=2E687802 -0=2E686619 1=2E189470 H > C-C_3 0 8=2E203195 -1=2E730281 0=2E179398 H > H-H_ 0 7=2E810295 -2=2E725868 0=2E189499 H > C-C_3 0 9=2E156898 -1=2E387924 -0=2E720561 H > H-H_ 0 9=2E517601 -2=2E112828 -1=2E419892 H > C-C_3 0 9=2E722192 0=2E044788 -0=2E735157 H > C-C_3 0 9=2E256796 0=2E966344 0=2E143252 H > H-H_ 0 9=2E641297 1=2E964615 0=2E125299 H > C-C_3 0 8=2E176324 0=2E575991 1=2E168464 H > S-S_R 0 6=2E456392 -1=2E144102 2=2E389675 H > C-C_R 0 10=2E816269 0=2E431492 -1=2E746270 H > O-O_R 0 11=2E276898 1=2E648657 -1=2E771447 H > O-O_R 0 11=2E326450 -0=2E546998 -2=2E655285 H > H-H_ 0 10=2E801854 -0=2E544241 -3=2E457655 H > > 1 25 1=2E0 26 1=2E0 34 1=2E0 35 1=2E0 37 1=2E0 38 1=2E0 > 2 3 1=2E0 5 1=2E0 10 1=2E0 11 1=2E0 14 1=2E0 20 1=2E0 > 3 4 1=2E0 7 1=2E0 11 1=2E0 14 1=2E0 15 1=2E0 > 4 5 1=2E0 14 1=2E0 15 1=2E0 18 1=2E0 24 1=2E0 > 5 14 1=2E0 20 1=2E0 23 1=2E0 24 1=2E0 > 6 7 1=2E0 9 1=2E0 11 1=2E0 13 1=2E0 27 1=2E0 29 1=2E0 > 7 8 1=2E0 11 1=2E0 13 1=2E0 15 1=2E0 > 8 13 1=2E0 15 1=2E0 17 1=2E0 27 1=2E0 33 1=2E0 > 9 10 1=2E0 11 1=2E0 12 1=2E0 28 1=2E0 29 1=2E0 > 10 11 1=2E0 12 1=2E0 19 1=2E0 20 1=2E0 > 11 > 12 19 1=2E0 28 1=2E0 > 13 27 1=2E0 > 14 > 15 17 1=2E0 18 1=2E0 49 1=2E0 > 16 17 1=2E0 18 1=2E0 26 1=2E0 35 1=2E0 > 17 18 1=2E0 33 1=2E0 35 1=2E0 > 18 24 1=2E0 26 1=2E0 > 19 20 1=2E0 21 1=2E0 28 1=2E0 36 1=2E0 > 20 21 1=2E0 23 1=2E0 > 21 22 1=2E0 23 1=2E0 36 1=2E0 38 1=2E0 > 22 23 1=2E0 25 1=2E0 38 1=2E0 > 23 24 1=2E0 25 1=2E0 > 24 25 1=2E0 26 1=2E0 > 25 26 1=2E0 38 1=2E0 > 26 35 1=2E0 > 27 29 1=2E0 31 1=2E0 33 1=2E0 > 28 29 1=2E0 30 1=2E0 36 1=2E0 > 29 30 1=2E0 31 1=2E0 > 30 31 1=2E0 32 1=2E0 36 1=2E0 37 1=2E0 > 31 32 1=2E0 33 1=2E0 34 1=2E0 > 32 34 1=2E0 37 1=2E0 > 33 34 1=2E0 35 1=2E0 > 34 35 1=2E0 37 1=2E0 > 35 > 36 37 1=2E0 38 1=2E0 > 37 38 1=2E0 > 38 > 39 48 1=2E0 > 40 41 1=2E0 48 2=2E0 49 1=2E0 > 41 43 2=2E0 42 1=2E0 > 42 > 43 45 1=2E0 44 1=2E0 > 44 > 45 46 2=2E0 50 1=2E0 > 46 48 1=2E0 47 1=2E0 > 47 > 48 > 49 > 50 51 1=2E5 52 1=2E0 > 51 > 52 53 1=2E0 > 53 > >The error: > > The polynomial fit failed=2E Using point 1=2E > A contracting polynomial of degree 16 produced 0=2E0000 > Search did not lower the energy significantly=2E > No lower point found -- run aborted=2E > Error termination via Lnk1e in >/apps/chpc/chem/gaussian16/B01/g16/linda-exe/l508=2Eexel at Wed Aug 21 >10:42:26 2019=2E > Job cpu time: 0 days 1 hours 0 minutes 59=2E3 seconds=2E > Elapsed time: 0 days 1 hours 21 minutes 10=2E0 seconds=2E >File lengths (MBytes): RWF=3D 63 Int=3D 0 D2E=3D 0 Chk=3D = 5 >Scr=3D 1 >failed to open execfile > > >Your help will be appreciated=2E > > >Kind regards > >Nikiwe Mhlanga > >Scientist > >Mintek > >Randburg > >South Africa --=20 =D0=9F=D1=80=D0=BE=D1=81=D1=82=D0=B8=D1=82=D0=B5 =D0=B7=D0=B0 =D0=BA=D1=80= =D0=B0=D1=82=D0=BA=D0=BE=D1=81=D1=82=D1=8C, =D1=81=D0=BE=D0=B7=D0=B4=D0=B0= =D0=BD=D0=BE =D0=B2 K-9 Mail=2E ------880OCRJMCT3D9ZMZGWH2G6VC5S3JUD Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Nikiwe,

This means that linear search = faoled, so You can try to avoid it by not using YQC, but, for example, XQC= =2E Another possible solution is to rise the SCF=3D(MaxNR=3DX) option value= to suppress calling the linear search (default is 2, You may try 1 or 0)= =2E Also, You can try adding IOp(5/6=3D2123) (which should try to avoid SD/= SSD (steepest descent/scaled steepest descent), but I am not sure anymore w= hat the first "2" meant and why it appeared in my notes)=2E

Regardin= g the ONIOM spheres=2E=2E=2E Shouldn't You probably be including at least t= hose Ag atoms directly connected to the mercapto acid in the high level of = calculation?

Best regards,
Igors Mihailovs
ISSP ULatvia
21 =D0=B0=D0=B2=D0=B3=D1=83=D1=81=D1=82=D0=B0 2= 019 =D0=B3=2E 17:02:56 GMT+03:00, "Nikiwe Mhlanga mhlanga=2Enikiwe,gmail=2E= com" <owner-chemistry._-_.ccl=2Enet> =D0=BF=D0=B8=D1=88=D0=B5=D1=82:
Dear CCL subscribers= ,

We ar= e using Gaussian16 to optimize and calculate frequency for a large meta= l system (4mercaptobenzoic acid chemisorbed on a silver cluster) using ONIO= M (QM/MM)=2E we are treating the high layer, mercaptobenzoic acid with QM a= nd low layer (Ag) with MM level of theory=2E

 

our input file 

%chk=3DAg38_MBA1=2Echk
%me= m =3D 5GB
%lindaworkers=3Dcnode0657=2Ecm=2Ecluster,cnode0906=2Ecm=2Eclus= ter
#p opt=3D(calcfc,tight) freq=3Draman oniom(pbepbe/lanl2dz:uff) geom= =3Dconnectivity int=3Dultrafine scf=3D(maxcycle=3D550,yqc,novaracc,vshift,f= ermi)

Chemisorption of 4-MBA via the S-end on Ag38

0 2 0 1 0 = 1
 Ag-              0   -0= =2E087538    3=2E780638   -2=2E135173 L
 Ag-   =            0    0=2E615213   -= 4=2E386287   -0=2E456889 L
 Ag-         &n= bsp;    0    2=2E829965   -3=2E263123    = ;1=2E265124 L H-H_     49
 Ag-        = ;      0    3=2E976204   -1=2E855176   -= 1=2E155020 L
 Ag-              0=    1=2E665691   -2=2E899508   -2=2E881852 L
 A= g-              0   -0=2E598942 &nb= sp; -1=2E649918    4=2E200849 L
 Ag-      =        0    2=2E333531   -2=2E041848 &n= bsp;  3=2E419830 L
 Ag-           &nb= sp;  0    2=2E789235    0=2E944243    3= =2E494113 L
 Ag-              0 =   -2=2E511342   -2=2E594676    2=2E814294 L
 Ag= -              0   -1=2E806843 &nbs= p; -4=2E057143    0=2E230665 L
 Ag-       =        0    0=2E168591   -3=2E740375 &nb= sp;  2=2E355867 L
 Ag-           &nbs= p;  0   -2=2E215108   -1=2E722228    0=2E605513 L<= br> Ag-              0    = ;0=2E819420   -0=2E269238    2=2E851871 L
 Ag-  = ;            0    1=2E680469  = -2=2E235243   -0=2E577234 L
 Ag-         =      0    4=2E283287   -0=2E732592   &nb= sp;1=2E589185 L H-H_     49
 Ag-       &nb= sp;      0    2=2E291430    1=2E736077 &= nbsp; -0=2E334834 L
 Ag-             =  0    3=2E746658    2=2E194141    1=2E51= 7127 L H-H_     49
 Ag-          = ;    0    4=2E316879    0=2E645926   -1= =2E013672 L
 Ag-              0 =   -3=2E610548   -2=2E155021   -1=2E294531 L
 Ag- &nb= sp;            0   -1=2E191423   -3= =2E274241   -2=2E498385 L
 Ag-         &nb= sp;    0   -2=2E731567   -0=2E932626   -3=2E350923= L
 Ag-              0   -0= =2E775108    0=2E272067   -2=2E677735 L
 Ag-   =            0    0=2E181427   -= 1=2E311149   -4=2E203277 L
 Ag-         &n= bsp;    0    2=2E763581   -0=2E242360   -3=2E= 306407 L
 Ag-              0 &nb= sp;  0=2E675001    1=2E666398   -3=2E983753 L
 = Ag-              0    2=2E5694= 25    2=2E593788   -2=2E565890 L
 Ag-     =          0   -0=2E079166    1=2E336= 138    4=2E402200 L
 Ag-         &nbs= p;    0   -4=2E249702   -0=2E625375    1=2E24= 1064 L
 Ag-              0  = ; -2=2E677469    0=2E262864    3=2E531853 L
 Ag= -              0   -3=2E842229 &nbs= p;  1=2E876387    1=2E383742 L
 Ag-     &n= bsp;        0   -1=2E565519    2=2E91664= 0    3=2E080574 L
 Ag-          =    0   -1=2E573313    2=2E331846    0= =2E753050 L
 Ag-              0 =    1=2E286577    3=2E308372    2=2E708779 L Ag-              0   -0=2E5= 27428    4=2E483001    0=2E690975 L
 Ag-  =            0    1=2E880836   =  4=2E076154   -0=2E015485 L
 Ag-       &nb= sp;      0   -4=2E041769    0=2E734748  = -1=2E324399 L
 Ag-              = ;0   -2=2E765623    3=2E335672   -1=2E063434 L
 = ;Ag-              0   -2=2E232937 &= nbsp;  2=2E088889   -3=2E215876 L
 H-H_     &nb= sp;       0    7=2E812188    1=2E301680 =    1=2E865590 H
 C-C_3          =  0    7=2E687802   -0=2E686619    1=2E189470= H
 C-C_3            0    8= =2E203195   -1=2E730281    0=2E179398 H
 H-H_  =           0    7=2E810295   -2=2E7= 25868    0=2E189499 H
 C-C_3         =    0    9=2E156898   -1=2E387924   -0=2E72056= 1 H
 H-H_             0    = 9=2E517601   -2=2E112828   -1=2E419892 H
 C-C_3   &n= bsp;        0    9=2E722192    0=2E= 044788   -0=2E735157 H
 C-C_3         &nbs= p;  0    9=2E256796    0=2E966344    0= =2E143252 H
 H-H_             0  = ;  9=2E641297    1=2E964615    0=2E125299 H
&nb= sp;C-C_3            0    8=2E176324=    0=2E575991    1=2E168464 H
 S-S_R   &n= bsp;        0    6=2E456392   -1=2E14410= 2    2=2E389675 H
 C-C_R         &nbs= p;  0   10=2E816269    0=2E431492   -1=2E746270 H<= br> O-O_R            0   11=2E27689= 8    1=2E648657   -1=2E771447 H
 O-O_R    =        0   11=2E326450   -0=2E546998   = -2=2E655285 H
 H-H_             0 &nb= sp; 10=2E801854   -0=2E544241   -3=2E457655 H

 1 25 1= =2E0 26 1=2E0 34 1=2E0 35 1=2E0 37 1=2E0 38 1=2E0
 2 3 1=2E0 5 1=2E= 0 10 1=2E0 11 1=2E0 14 1=2E0 20 1=2E0
 3 4 1=2E0 7 1=2E0 11 1=2E0 1= 4 1=2E0 15 1=2E0
 4 5 1=2E0 14 1=2E0 15 1=2E0 18 1=2E0 24 1=2E0
=  5 14 1=2E0 20 1=2E0 23 1=2E0 24 1=2E0
 6 7 1=2E0 9 1=2E0 11 1= =2E0 13 1=2E0 27 1=2E0 29 1=2E0
 7 8 1=2E0 11 1=2E0 13 1=2E0 15 1= =2E0
 8 13 1=2E0 15 1=2E0 17 1=2E0 27 1=2E0 33 1=2E0
 9 10 = 1=2E0 11 1=2E0 12 1=2E0 28 1=2E0 29 1=2E0
 10 11 1=2E0 12 1=2E0 19 = 1=2E0 20 1=2E0
 11
 12 19 1=2E0 28 1=2E0
 13 27 1= =2E0
 14
 15 17 1=2E0 18 1=2E0 49 1=2E0
 16 17 1=2E= 0 18 1=2E0 26 1=2E0 35 1=2E0
 17 18 1=2E0 33 1=2E0 35 1=2E0
&nbs= p;18 24 1=2E0 26 1=2E0
 19 20 1=2E0 21 1=2E0 28 1=2E0 36 1=2E0
&= nbsp;20 21 1=2E0 23 1=2E0
 21 22 1=2E0 23 1=2E0 36 1=2E0 38 1=2E0 22 23 1=2E0 25 1=2E0 38 1=2E0
 23 24 1=2E0 25 1=2E0
&nbs= p;24 25 1=2E0 26 1=2E0
 25 26 1=2E0 38 1=2E0
 26 35 1=2E0 27 29 1=2E0 31 1=2E0 33 1=2E0
 28 29 1=2E0 30 1=2E0 36 1=2E= 0
 29 30 1=2E0 31 1=2E0
 30 31 1=2E0 32 1=2E0 36 1=2E0 37 1= =2E0
 31 32 1=2E0 33 1=2E0 34 1=2E0
 32 34 1=2E0 37 1=2E0 33 34 1=2E0 35 1=2E0
 34 35 1=2E0 37 1=2E0
 35
&= nbsp;36 37 1=2E0 38 1=2E0
 37 38 1=2E0
 38
 39 48 1= =2E0
 40 41 1=2E0 48 2=2E0 49 1=2E0
 41 43 2=2E0 42 1=2E0 42
 43 45 1=2E0 44 1=2E0
 44
 45 46 2=2E0 5= 0 1=2E0
 46 48 1=2E0 47 1=2E0
 47
 48
 49 50 51 1=2E5 52 1=2E0
 51
 52 53 1=2E0
 53

The error:

 = ;The polynomial fit failed=2E  Using point  1=2E
   =  A contracting polynomial of degree 16 produced  0=2E0000
&nb= sp;Search did not lower the energy significantly=2E
 No lower point= found -- run aborted=2E
 Error termination via Lnk1e in /apps/chpc= /chem/gaussian16/B01/g16/linda-exe/l508=2Eexel at Wed Aug 21 10:42:26 2019= =2E
 Job cpu time:       0 days  1 hours  = 0 minutes 59=2E3 seconds=2E
 Elapsed time:       0 d= ays  1 hours 21 minutes 10=2E0 seconds=2E
 File lengths (MByte= s):  RWF=3D     63 Int=3D      0 D2E=3D  = ;    0 Chk=3D      5 Scr=3D      1<= br>failed to open execfile


Your help will be appreciated=2E


<= /p>

Kind regards

Nikiwe Mhl= anga

Scientist

Mintek

Randburg

South Africa





--
=D0=9F=D1=80=D0=BE=D1=81=D1=82=D0=B8=D1=82= =D0=B5 =D0=B7=D0=B0 =D0=BA=D1=80=D0=B0=D1=82=D0=BA=D0=BE=D1=81=D1=82=D1=8C,= =D1=81=D0=BE=D0=B7=D0=B4=D0=B0=D0=BD=D0=BE =D0=B2 K-9 Mail=2E ------880OCRJMCT3D9ZMZGWH2G6VC5S3JUD-- From owner-chemistry@ccl.net Thu Aug 22 11:26:01 2019 From: "Nandan Kumar nandanchotu71|,|gmail.com" To: CCL Subject: CCL: ONIOM problem while doing the optimization: QM/MM ? Message-Id: <-53820-190822010659-18245-wCib3HVKnhRCzNk1pDdBcg~~server.ccl.net> X-Original-From: "Nandan Kumar" Date: Thu, 22 Aug 2019 01:06:55 -0400 Sent to CCL by: "Nandan Kumar" [nandanchotu71^^gmail.com] Hello everyone, I'm trying to run a ONIOM geometry optimization using b3lyp:amber oniom method. But it ends up with an error, which look like this GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. Internal Forces: Max 0.199665420 RMS 0.023405890 Search for a local minimum. Step number 1 out of a maximum of 1106 All quantities printed in internal units (Hartrees-Bohrs-Radians) NRF ne Abs NRFX Error termination via Lnk1e in /opt/g16/l103.exe at Thu Aug 22 02:53:25 2019. Please help me to solve this problem.