From owner-chemistry@ccl.net Mon Apr 1 08:26:00 2019 From: "Nikiwe Mhlanga mhlanga.nikiwe|gmail.com" To: CCL Subject: CCL: How to parameterize uff for fcc metals e.g silver on ONIOM calculation where the metal is part of the real system Message-Id: <-53666-190401040902-26177-I3k48TuDE+I0kE/tsDf+cQ_-_server.ccl.net> X-Original-From: Nikiwe Mhlanga Content-Type: multipart/alternative; boundary="0000000000003971550585738812" Date: Mon, 1 Apr 2019 10:08:31 +0200 MIME-Version: 1.0 Sent to CCL by: Nikiwe Mhlanga [mhlanga.nikiwe : gmail.com] --0000000000003971550585738812 Content-Type: text/plain; charset="UTF-8" Dear CCL subscribers, We are using ONIOM to calculate vibrational frequencies of a sodium citrate molecule adsorbed on a Ag NPs with 923 atoms. The citrate moiety is our high layer treated with DFT (QM) and all the Ag atoms are our low layer treated with MM level of theory. The output file does not have an error message yet the system does not converge, calculation seems to be cut off in less than a minute. To try and solve the issue we have tried to increase memory from 5 GB to 10 GB and the issue was not solved. We think the source of the issue could be the uff failing to configure parameters for the low layer (The Ag-Ag) bonds. our route section is as follows, %chk=AgCit1_P.chk %lindaworkers=cnode0494.cm.cluster,cnode0485.cm.cluster %Mem=50000MB %nproc=24 #p Opt freq=Raman oniom(B3LYP/6-311++g(d,p) EmpiricalDispersion=GD3BJ:uff)=embed geom=connectivity The last line on the output file which does not show an error looks like this, Atom 941 942 943 IAtWgt= 1 1 1 AtmWgt= 1.0078250 1.0078250 1.0078250 NucSpn= 1 1 1 AtZEff= -0.0000000 -0.0000000 -0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 NMagM= 2.7928460 2.7928460 2.7928460 AtZNuc= 1.0000000 1.0000000 1.0000000 Generating MM parameters. Your help will be appreciated. Kind regards Nikiwe Mhlanga Scientist Mintek Randburg South Africa --0000000000003971550585738812 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear CCL subscribers,

=

We are using ONIOM to = calculate vibrational frequencies of a sodium citrate molecule adsorbed on = a Ag NPs with =C2=A0923 atoms.=C2=A0 The citrate moiety is our high layer t= reated with DFT (QM) and all the Ag atoms are our low layer treated with MM= =C2=A0level of theory.=C2=A0 The output file does not have an error messag= e yet the system does not converge, calculation seems to be cut =C2=A0off i= n less than a minute. To try and solve the issue we have tried to increase = memory from 5 GB to 10 GB and the issue was not solved.


We think the=C2=A0source of the issue= could be the uff failing to configure parameters for the low layer (The Ag= -Ag) bonds.=C2=A0


our route section is as follows, =C2=A0

%chk=3DA= gCit1_P.chk
%lindaworkers=3Dcnode0494.cm.cluster,cnode0485.cm.cluster%Mem=3D50000MB
%nproc=3D24
#p Opt freq=3DRaman oniom(B3LYP/6-311++g(= d,p) EmpiricalDispersion=3DGD3BJ:uff)=3Dembed=C2=A0 geom=3Dconnectivity

=


The last line on the = output file which does not show an error looks like this,

=C2=A0 Atom=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 941=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 942=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 943
=C2=A0IAtWgt=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 1=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 1=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1=C2=A0AtmWgt=3D=C2=A0=C2=A0 1.0078250=C2=A0=C2=A0 1.0078250=C2=A0=C2=A0 1= .0078250
=C2=A0NucSpn=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 1=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 1=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1
=C2=A0At= ZEff=3D=C2=A0 -0.0000000=C2=A0 -0.0000000=C2=A0 -0.0000000
=C2=A0NQMom= =3D=C2=A0=C2=A0=C2=A0 0.0000000=C2=A0=C2=A0 0.0000000=C2=A0=C2=A0 0.0000000=
=C2=A0NMagM=3D=C2=A0=C2=A0=C2=A0 2.7928460=C2=A0=C2=A0 2.7928460=C2=A0= =C2=A0 2.7928460
=C2=A0AtZNuc=3D=C2=A0=C2=A0 1.0000000=C2=A0=C2=A0 1.000= 0000=C2=A0=C2=A0 1.0000000
=C2=A0Generating MM parameters.


Your help will be appreciated= .


Kind regards

=

Nikiwe Mhlanga

Scientist

Mintek

Randburg

South Africa







--0000000000003971550585738812-- From owner-chemistry@ccl.net Mon Apr 1 16:11:01 2019 From: "Peter Kraus peter.kraus_._geeksonbikes.net" To: CCL Subject: CCL: How to parameterize uff for fcc metals e.g silver on ONIOM calculation where the metal is part of the real system Message-Id: <-53667-190401160851-22195-KVxv/chnu9XZDecI+fRKAw() server.ccl.net> X-Original-From: Peter Kraus Content-Type: multipart/alternative; boundary="00000000000050496305857d962e" Date: Mon, 1 Apr 2019 22:08:31 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Kraus [peter.kraus/a\geeksonbikes.net] --00000000000050496305857d962e Content-Type: text/plain; charset="UTF-8" Dear Dr. Nikiwe Mhlanga, personally, I've had quite poor experiences when trying to apply ONIOM to metal-containing systems. In my case it was Pt in the "low" region (PM6) and DFT for a small Pt core and adsorbed organics. The calculation never converged: it was oscillating in the SCF energy. Back when I was trying, I have not seen any result where ONIOM was successful for metallic systems - but that was 6 years ago, it might have changed since then. While it's not a solution, perhaps you could give CP2K a shot. With it, you might be able to afford a full GGA-DFT calculation for your system, less than 1000 atoms are not that many. I would definitely not use BLYP/B3LYP for bulk metallic systems, they were modelled after the He atom and are not good for extended metals that are supposedly closer to the electron gas limit. If you are keen on combining two levels of theory (QM and MM), CP2K has a good manual on the topic, with what might be a similar system, here: https://www.cp2k.org/exercises:2017_ethz_mmm:qmmm CP2K is, of course, open source. Best regards, Peter On Mon, 1 Apr 2019 at 16:10, Nikiwe Mhlanga mhlanga.nikiwe|gmail.com < owner-chemistry{:}ccl.net> wrote: > Dear CCL subscribers, > > We are using ONIOM to calculate vibrational frequencies of a sodium > citrate molecule adsorbed on a Ag NPs with 923 atoms. The citrate moiety > is our high layer treated with DFT (QM) and all the Ag atoms are our low > layer treated with MM level of theory. The output file does not have an > error message yet the system does not converge, calculation seems to be cut > off in less than a minute. To try and solve the issue we have tried to > increase memory from 5 GB to 10 GB and the issue was not solved. > > > We think the source of the issue could be the uff failing to configure > parameters for the low layer (The Ag-Ag) bonds. > > > our route section is as follows, > > %chk=AgCit1_P.chk > %lindaworkers=cnode0494.cm.cluster,cnode0485.cm.cluster > %Mem=50000MB > %nproc=24 > #p Opt freq=Raman oniom(B3LYP/6-311++g(d,p) > EmpiricalDispersion=GD3BJ:uff)=embed geom=connectivity > > > The last line on the output file which does not show an error looks like > this, > > Atom 941 942 943 > IAtWgt= 1 1 1 > AtmWgt= 1.0078250 1.0078250 1.0078250 > NucSpn= 1 1 1 > AtZEff= -0.0000000 -0.0000000 -0.0000000 > NQMom= 0.0000000 0.0000000 0.0000000 > NMagM= 2.7928460 2.7928460 2.7928460 > AtZNuc= 1.0000000 1.0000000 1.0000000 > Generating MM parameters. > > > Your help will be appreciated. > > > Kind regards > > Nikiwe Mhlanga > > Scientist > > Mintek > > Randburg > > South Africa > > > > > > > > -- Sent from your iPhone. No, really. --00000000000050496305857d962e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Dr. Nikiwe Mhlanga,
<= br>
personally, I've had quite poor experiences when trying t= o apply ONIOM to metal-containing systems. In my case it was Pt in the &quo= t;low" region (PM6) and DFT for a small Pt core and adsorbed organics.= The calculation never converged: it was oscillating in the SCF energy. Bac= k when I was trying, I have not seen any result where ONIOM was successful = for metallic systems - but that was 6 years ago, it might have changed sinc= e then.

While it's not a solution, perhaps= you could give CP2K a shot. With it, you might be able to afford a full GG= A-DFT calculation for your system, less than 1000 atoms are not that many. = I would definitely not use BLYP/B3LYP for bulk metallic systems, they were = modelled after the He atom and are not good for extended metals that are su= pposedly closer to the electron gas limit.

If = you are keen on combining two levels of theory (QM and MM), CP2K has a good= manual on the topic, with what might be a similar system, here:
=

CP2K is, of course, open source.

Best regard= s,
Peter


On Mon, 1 Apr 2019 at 16:1= 0, Nikiwe Mhlanga mhlanga.nikiwe|gmail.com= <owner-chemistry{:}ccl.net= > wrote:
Dear CCL subscribers,

We are using ONIOM to calc= ulate vibrational frequencies of a sodium citrate molecule adsorbed on a Ag= NPs with =C2=A0923 atoms.=C2=A0 The citrate moiety is our high layer treat= ed with DFT (QM) and all the Ag atoms are our low layer treated with MM =C2= =A0level of theory.=C2=A0 The output file does not have an error message ye= t the system does not converge, calculation seems to be cut =C2=A0off in le= ss than a minute. To try and solve the issue we have tried to increase memo= ry from 5 GB to 10 GB and the issue was not solved.


We think the=C2=A0source of the issue cou= ld be the uff failing to configure parameters for the low layer (The Ag-Ag)= bonds.=C2=A0


our= route section is as follows, =C2=A0

%chk=3DAgCit= 1_P.chk
%lindaworkers=3Dcnode0494.cm.cluster,cnode0485.cm.cluster
%Me= m=3D50000MB
%nproc=3D24
#p Opt freq=3DRaman oniom(B3LYP/6-311++g(d,p)= EmpiricalDispersion=3DGD3BJ:uff)=3Dembed=C2=A0 geom=3Dconnectivity


The last line on the outp= ut file which does not show an error looks like this,

=C2=A0 Atom=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 941=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 942=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 943
=C2=A0IAtWgt=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 1=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 1=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1
= =C2=A0AtmWgt=3D=C2=A0=C2=A0 1.0078250=C2=A0=C2=A0 1.0078250=C2=A0=C2=A0 1.0= 078250
=C2=A0NucSpn=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 1=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 = 1=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1
=C2=A0At= ZEff=3D=C2=A0 -0.0000000=C2=A0 -0.0000000=C2=A0 -0.0000000
=C2=A0NQMom= =3D=C2=A0=C2=A0=C2=A0 0.0000000=C2=A0=C2=A0 0.0000000=C2=A0=C2=A0 0.0000000=
=C2=A0NMagM=3D=C2=A0=C2=A0=C2=A0 2.7928460=C2=A0=C2=A0 2.7928460=C2=A0= =C2=A0 2.7928460
=C2=A0AtZNuc=3D=C2=A0=C2=A0 1.0000000=C2=A0=C2=A0 1.000= 0000=C2=A0=C2=A0 1.0000000
=C2=A0Generating MM parameters.


Your help will be appreciated= .


Kind regards

=

Nikiwe Mhlanga

Scientist

Mintek

Randburg

South Africa









--
Sent from your iPhone. No, really.
--00000000000050496305857d962e--