From owner-chemistry@ccl.net Thu Dec 5 13:22:00 2024 From: "Theo de Bruin theodorus.de-bruin]-[ifpen.fr" To: CCL Subject: CCL:G: keep bond aligned along an axis during geometry optimization in G16 Message-Id: <-55260-241205102509-16058-Ly3doBBQ6NbyLHD4SQFY4Q:server.ccl.net> X-Original-From: "Theo de Bruin" Date: Thu, 5 Dec 2024 10:25:07 -0500 Sent to CCL by: "Theo de Bruin" [theodorus.de-bruin * ifpen.fr] Dear all, I want to study the impact of an electric field on specific bond a molecule. Therefore, I have aligned that bond along the Z-axis, but during the geometry optimization, the molecule gets reorientated (-> standard orientation) and the bond is not aligned anymore to the axis of the Efield. The most intuitive way to correct this, would be to freeze the Cartesian coordinates of one atom at (0,0,0) and freeze x=0.0 and y=0.0 for the 2nd atom of the bond. Yet, Gaussian does not allow to do this, or at least I don't know the right syntax for this. Do you have any suggestions that conserve the alignment during geometry optimizations in Gaussian 16? Thanks in advance, Best regards, Theo From owner-chemistry@ccl.net Thu Dec 5 16:30:00 2024 From: "Geoffrey Hutchison geoff.hutchison * gmail.com" To: CCL Subject: CCL:G: keep bond aligned along an axis during geometry optimization in G16 Message-Id: <-55261-241205162136-30221-8p3/62L4ZFLtKBdTWfs0pA(~)server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Type: multipart/alternative; boundary="00000000000042272b06288c7b46" Date: Thu, 5 Dec 2024 13:21:28 -0800 MIME-Version: 1.0 (Mimestream 1.4.2) Sent to CCL by: Geoffrey Hutchison [geoff.hutchison#,#gmail.com] --00000000000042272b06288c7b46 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable If you want to stop Gaussian from re-orienting coordinates, you want the NoSymm keyword. Best, -Geoff --- Prof. Geoffrey Hutchison (he/him) Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh]_[pitt.edu web: https://hutchisonlab.org/ On Dec 5, 2024 at 10:25:07=E2=80=AFAM, Theo de Bruin theodorus.de-bruin]-[i= fpen.fr < owner-chemistry]_[ccl.net> wrote: > > Sent to CCL by: "Theo de Bruin" [theodorus.de-bruin * ifpen.fr] > Dear all, > > I want to study the impact of an electric field on specific bond a > molecule. > Therefore, I have aligned that bond along the Z-axis, but during the > geometry > optimization, the molecule gets reorientated (-> standard orientation) an= d > the > bond is not aligned anymore to the axis of the Efield. > The most intuitive way to correct this, would be to freeze the Cartesian > coordinates of one atom at (0,0,0) and freeze x=3D0.0 and y=3D0.0 for the= 2nd > atom > of the bond. > > Yet, Gaussian does not allow to do this, or at least I don't know the > right > syntax for this. > > Do you have any suggestions that conserve the alignment during geometry > optimizations in Gaussian 16? > > Thanks in advance, > Best regards, Theo > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --00000000000042272b06288c7b46 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
If you want to stop Gaussian from re-orienting coordinates, you want th= e NoSymm keyword.

Best,
-Geoff

=C2=A0---
Prof. Geoffrey Hutchison (he/him)
Department of Chemistry
University of P= ittsburgh
tel: (412) 648-0492
e= mail: geoffh]_[pitt.edu
web: https://hutchisonlab.or= g/=C2=A0

On Dec 5, 2024 at 10:25:07=E2=80= =AFAM, Theo de Bruin theodorus.de-bruin]-[ifpen= .fr <owner-chemistry]_[ccl.= net> wrote:
=20

Sent to CCL by: "Theo =C2=A0de Bruin" [theodorus.de-bruin= * ifpen.fr]
Dear all,

I want to = study the impact of an electric field on specific bond a molecule.
Ther= efore, I have aligned that bond along the Z-axis, but during the geometry <= br>optimization, the molecule gets reorientated (-> standard orientation= ) and the
bond is not aligned anymore to the axis of the Efield.
Th= e most intuitive way to correct this, would be to freeze the Cartesian
= coordinates of one atom at (0,0,0) and freeze x=3D0.0 and y=3D0.0 for the 2= nd atom
of the bond.

Yet, Gaussian does not allow to do this, or= at least I don't know the right
syntax for this.

Do you hav= e any suggestions that conserve the alignment during geometry
optimizat= ions in Gaussian 16?

Thanks in advance,
Best regards, Theo


-=3D This is automatically added to each message by the mailing sc= ript =3D-
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--00000000000042272b06288c7b46-- From owner-chemistry@ccl.net Thu Dec 5 17:05:01 2024 From: "Frank Jensen frj*_*chem.au.dk" To: CCL Subject: CCL:G: keep bond aligned along an axis during geometry optimization in G16 Message-Id: <-55262-241205164323-2935-DyzXJug9UviT/t26J3A7aw(0)server.ccl.net> X-Original-From: Frank Jensen Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 5 Dec 2024 21:43:08 +0000 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj~~chem.au.dk] I can think of two options: 1) Fix the Cartesian coordinate of one atom at 0,0,0 using the geom=addredundant or opt=addredundant option, place the second atom along the z-axis, and turn off symmetry by using the nosymm keyword. This may fail if you are having a 'large' molecule and/or not a field along the z-axis and performing an optimization, as the optimization can break the z-alignment. 2) Construct a z-matrix where all your constraint variables are explicitly defined, turn off symmetry (nosymm) and use opt=z-matrix to perform the optimization in your defined internal coordinates. By using a proper amount of dummy atoms (= points in space) and splitting your variables into variable (=optimizable) and fixed (= non optimizable) sets, this should do the trick. Frank Frank Jensen Assoc. Prof. Department of Chemistry Aarhus University https://tildeweb.au.dk/au23758/ https://pure.au.dk/portal/en/frj!A!chem.au.dk -----Original Message----- > From: owner-chemistry+frj==chem.au.dk!A!ccl.net On Behalf Of Theo de Bruin theodorus.de-bruin]-[ifpen.fr Sent: Thursday, December 5, 2024 4:25 PM To: Frank Jensen Subject: CCL:G: keep bond aligned along an axis during geometry optimization in G16 Sent to CCL by: "Theo de Bruin" [theodorus.de-bruin * ifpen.fr] Dear all, I want to study the impact of an electric field on specific bond a molecule. Therefore, I have aligned that bond along the Z-axis, but during the geometry optimization, the molecule gets reorientated (-> standard orientation) and the bond is not aligned anymore to the axis of the Efield. The most intuitive way to correct this, would be to freeze the Cartesian coordinates of one atom at (0,0,0) and freeze x=0.0 and y=0.0 for the 2nd atom of the bond. Yet, Gaussian does not allow to do this, or at least I don't know the right syntax for this. Do you have any suggestions that conserve the alignment during geometry optimizations in Gaussian 16? Thanks in advance, Best regards, Theohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml/http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Dec 5 23:06:00 2024 From: "Martin C. Schwarzer schwarzer|a|mail.de" To: CCL Subject: CCL:G: =?US-ASCII?Q?Re=3A_CCL=3AG=3A_keep_bond_aligned_along_an_a?= =?US-ASCII?Q?xis_during_geometry_optimization_in_G16?= Message-Id: <-55263-241205174245-26643-jbP6fTte9h0bTMdhUivkUQ**server.ccl.net> X-Original-From: "Martin C. Schwarzer" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Thu, 05 Dec 2024 23:42:30 +0100 MIME-Version: 1.0 Sent to CCL by: "Martin C. Schwarzer" [schwarzer---mail.de] Hallöchen Theo, You probably want to try the "new" (g16 is 8 years old now!) generalised internal coordinates (GIC). I think I've written a few words about that here: Have fun and good luck, Martin -- Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet. On 5 December 2024 16:25:07 CET, "Theo de Bruin theodorus.de-bruin]-[ifpen.fr" wrote: > >Sent to CCL by: "Theo de Bruin" [theodorus.de-bruin * ifpen.fr] >Dear all, > >I want to study the impact of an electric field on specific bond a molecule. >Therefore, I have aligned that bond along the Z-axis, but during the geometry >optimization, the molecule gets reorientated (-> standard orientation) and the >bond is not aligned anymore to the axis of the Efield. >The most intuitive way to correct this, would be to freeze the Cartesian >coordinates of one atom at (0,0,0) and freeze x=0.0 and y=0.0 for the 2nd atom >of the bond. > >Yet, Gaussian does not allow to do this, or at least I don't know the right >syntax for this. > >Do you have any suggestions that conserve the alignment during geometry >optimizations in Gaussian 16? > >Thanks in advance, >Best regards, Theo> >