From owner-chemistry@ccl.net Fri Mar 20 11:06:01 2015 From: "Safiya Ess Amer amersaf85|,|yahoo.com" To: CCL Subject: CCL:G: problem in Gaussian 03 program Message-Id: <-51159-150320101619-3112-+gA8Eam0qFCSFnFgsNmH1Q-$-server.ccl.net> X-Original-From: "Safiya Ess Amer" Date: Fri, 20 Mar 2015 10:16:18 -0400 Sent to CCL by: "Safiya Ess Amer" [amersaf85!=!yahoo.com] Hello for all I am using G03W to get results of a system H2-Fe(OH)3. I want to change the positions of two hydrogen atoms in Z direction and get energy at each position. How can I use scan keyword to move more than one atom at the same time (as two hydrogen atoms mentioned above). Thanks in advance Safiya Amer amersaf85*yahoo.com From owner-chemistry@ccl.net Fri Mar 20 12:46:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor|fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: problem in Gaussian 03 program Message-Id: <-51160-150320124451-5572-eBXKVsu5nkMd4ZmAXZEk6w%a%server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 20 Mar 2015 17:40:04 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor=fluor.quimica.uniovi.es] On Fri, Mar 20, 2015 at 10:16:18AM -0400, Safiya Ess Amer amersaf85|,|yahoo.com wrote: > > Sent to CCL by: "Safiya Ess Amer" [amersaf85!=!yahoo.com] > Hello for all > I am using G03W to get results of a system H2-Fe(OH)3. I want to change the > positions of two hydrogen atoms in Z direction and get energy at each position. > How can I use scan keyword to move more than one atom at the same time > (as two hydrogen atoms mentioned above). Safiya, The best approach is to create by yourselft the geometries you want to explore and let the computer code of your election provide you the energies of the system. To create the geometries I recommend you an scripting language (python, matlab, octave, Mathematica, ...) There are tools to explore the geometries yoou want to examine. There are even tools to analyze the posible geomettries using force fields. Not necesarily the best tool but I like lately avogadro. Surely other scientists may recommend you more moderne or user friendly tools. Best regards, Dr. Víctor Luaña -- . . "The hardest part in solving a problem is recognizing / `' \ its existence. Learning the causes CAN be the road to /(o)(o)\ the solution." /`. \/ .'\ -- ¿? / '`'` \ "Lo mediocre es peor que lo bueno, pero también es peor | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una | |'`'`| | actitud" \/`'`'`'\/ -- Jorge Wasenberg, 2015 ===(((==)))==================================+========================= ! Dr.Víctor Luaña ! Mediocre is worse than ! Departamento de Química Física y Analítica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor#%#fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Fri Mar 20 13:31:00 2015 From: "Yingbin Ge yingbin.ge\a/gmail.com" To: CCL Subject: CCL:G: problem in Gaussian 03 program Message-Id: <-51161-150320132914-23045-TTv3DcpCgZwBb8M8qdVVzQ~~server.ccl.net> X-Original-From: Yingbin Ge Content-Type: multipart/alternative; boundary=001a114232f26583720511bba79d Date: Fri, 20 Mar 2015 10:29:08 -0700 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge^gmail.com] --001a114232f26583720511bba79d Content-Type: text/plain; charset=UTF-8 Safiya, I think Gaussian allows the use of ghost atoms, which have no mass and no charge. You may simply define a ghost atom in the center of the H2 and scan the distance between the ghost atom and the Fe ion. You may also freeze the distance between the ghost atom and Fe to be 3 angstrom and run an optimization calculation with the constraint. Then you ran the same contrainted optimization calculations at 2.5, 2, and 1.5 angstroms, etc. I'd prefer the 2nd way, which requires more computational time but can have all other geometric parameters (except for the distance between H2 and Fe) optimized. Sincerely, Yingbin Yingbin Ge, Associate Professor Science Building 207A Department of Chemistry Central Washington University 400 E University Way Ellensburg, WA 98926 Office Phone: 509-963-2817 On Fri, Mar 20, 2015 at 7:16 AM, Safiya Ess Amer amersaf85|,|yahoo.com < owner-chemistry_+_ccl.net> wrote: > > Sent to CCL by: "Safiya Ess Amer" [amersaf85!=!yahoo.com] > Hello for all > I am using G03W to get results of a system H2-Fe(OH)3. I want to change the > positions of two hydrogen atoms in Z direction and get energy at each > position. > How can I use scan keyword to move more than one atom at the same time (as > two > hydrogen atoms mentioned above). > > Thanks in advance > > Safiya Amer > amersaf85_-_yahoo.com> > > --001a114232f26583720511bba79d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Safiya,

I t= hink Gaussian allows the use of ghost atoms, which have no mass and no char= ge. You may simply define a ghost atom in the center of the H2 and scan the= distance between the ghost atom and the Fe ion.

You may also freeze the distance between the ghost atom and Fe to be 3 ang= strom and run an optimization calculation with the constraint. Then you ran= the same contrainted optimization calculations at 2.5, 2, and 1.5 angstrom= s, etc.

I'd prefer the 2nd way, which re= quires more computational time but can have all other geometric parameters = (except for the distance between H2 and Fe) optimized.

Sincerely,
Yingbin

Yingbin Ge, Associate Professor
Science Building 207A
Department of Chemistry
Central Washington University
400 E University Way
Ellensburg, WA 98926
Office Phone: 509-963-2817

On Fri, M= ar 20, 2015 at 7:16 AM, Safiya Ess Amer amersaf85|,|yahoo.com <owner-chemistry_+_ccl.net> wrote:

Sent to CCL by: "Safiya Ess Amer" [amersaf85!=3D!yahoo.com]
Hello for all
I am using G03W to get results of a system H2-Fe(OH)3. I want to change the=
positions of two hydrogen atoms in Z direction and get energy at each posit= ion.
How can I use scan keyword to move more than one atom at the same time (as = two
hydrogen atoms mentioned above).

Thanks in advance

Safiya Amer
amersaf85_-_yaho= o.com



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--001a114232f26583720511bba79d-- From owner-chemistry@ccl.net Fri Mar 20 17:32:00 2015 From: "Safiya Ess Amer amersaf85**yahoo.com" To: CCL Subject: CCL:G: problem in Gaussian 03 program Message-Id: <-51162-150320172601-8415-MuaDzMIs7QHSJJYYALGEcw.@.server.ccl.net> X-Original-From: "Safiya Ess Amer" Date: Fri, 20 Mar 2015 17:25:59 -0400 Sent to CCL by: "Safiya Ess Amer" [amersaf85**yahoo.com] > "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor|fluor.quimica.uniovi.es" wrote: > > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor=fluor.quimica.uniovi.es] > On Fri, Mar 20, 2015 at 10:16:18AM -0400, Safiya Ess Amer amersaf85|,|yahoo.com wrote: > > > > Sent to CCL by: "Safiya Ess Amer" [amersaf85!=!yahoo.com] > > Hello for all > > I am using G03W to get results of a system H2-Fe(OH)3. I want to change the > > positions of two hydrogen atoms in Z direction and get energy at each position. > > How can I use scan keyword to move more than one atom at the same time > > (as two hydrogen atoms mentioned above). > > Safiya, > > The best approach is to create by yourselft the geometries you > want to explore and let the computer code of your election provide you > the energies of the system. > > To create the geometries I recommend you an scripting language (python, > matlab, octave, Mathematica, ...) There are tools to explore the geometries > yoou want to examine. There are even tools to analyze the posible geomettries > using force fields. Not necesarily the best tool but I like lately avogadro. > > > Surely other scientists may recommend you more moderne or user friendly > tools. > > Best regards, > Dr. Vctor Luaa > -- > . . "The hardest part in solving a problem is recognizing > / `' \ its existence. Learning the causes CAN be the road to > /(o)(o)\ the solution." > /`. \/ .'\ -- ? > / '`'` \ "Lo mediocre es peor que lo bueno, pero tambin es peor > | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una > | |'`'`| | actitud" > \/`'`'`'\/ -- Jorge Wasenberg, 2015 > ===(((==)))==================================+========================= > ! Dr.Vctor Luaa ! Mediocre is worse than > ! Departamento de Qumica Fsica y Analtica ! good, but it is also > ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because > ! e-mail: victor#%#fluor.quimica.uniovi.es ! mediocrity is not a grade, > ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude > +--------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) > > Thanks to reply Dr. Vctor Luaa The geometry is not problem with my system, I use GaussView to visualize it, that is easy but the problem about movement of two hydrogen atoms of H2 molecule above Fe ion. I put suitable coordinates of all atoms of the system with freezing and ran program to get energy. The positions of H2 atoms changed manually each time. I need a way with automaticaly changing for positions. best regards. From owner-chemistry@ccl.net Fri Mar 20 19:22:00 2015 From: "Safiya Ess Amer amersaf85(a)yahoo.com" To: CCL Subject: CCL:G: problem in Gaussian 03 program Message-Id: <-51163-150320183919-30853-weik1fAThZGYFFhPG6tFKA\a/server.ccl.net> X-Original-From: "Safiya Ess Amer" Date: Fri, 20 Mar 2015 18:39:17 -0400 Sent to CCL by: "Safiya Ess Amer" [amersaf85_._yahoo.com] > "Yingbin Ge yingbin.ge\a/gmail.com" wrote: > > Sent to CCL by: Yingbin Ge [yingbin.ge^gmail.com] > --001a114232f26583720511bba79d > Content-Type: text/plain; charset=UTF-8 > > Safiya, > > I think Gaussian allows the use of ghost atoms, which have no mass and no > charge. You may simply define a ghost atom in the center of the H2 and scan > the distance between the ghost atom and the Fe ion. > > You may also freeze the distance between the ghost atom and Fe to be 3 > angstrom and run an optimization calculation with the constraint. Then you > ran the same contrainted optimization calculations at 2.5, 2, and 1.5 > angstroms, etc. > > I'd prefer the 2nd way, which requires more computational time but can have > all other geometric parameters (except for the distance between H2 and Fe) > optimized. > > Sincerely, > Yingbin > > Yingbin Ge, Associate Professor > Science Building 207A > Department of Chemistry > Central Washington University > 400 E University Way > Ellensburg, WA 98926 > Office Phone: 509-963-2817 > > > On Fri, Mar 20, 2015 at 7:16 AM, Safiya Ess Amer amersaf85|,|yahoo.com < > owner-chemistry_+_ccl.net> wrote: > > > > > Sent to CCL by: "Safiya Ess Amer" [amersaf85!=!yahoo.com] > > Hello for all > > I am using G03W to get results of a system H2-Fe(OH)3. I want to change the > > positions of two hydrogen atoms in Z direction and get energy at each > > position. > > How can I use scan keyword to move more than one atom at the same time (as > > two > > hydrogen atoms mentioned above). > > > > Thanks in advance > > > > Safiya Amer > > amersaf85_-_yahoo.com> > > > > > > --001a114232f26583720511bba79d > Content-Type: text/html; charset=UTF-8 > Content-Transfer-Encoding: quoted-printable > >
Safiya,

I t= > hink Gaussian allows the use of ghost atoms, which have no mass and no char= > ge. You may simply define a ghost atom in the center of the H2 and scan the= > distance between the ghost atom and the Fe ion.

>You may also freeze the distance between the ghost atom and Fe to be 3 ang= > strom and run an optimization calculation with the constraint. Then you ran= > the same contrainted optimization calculations at 2.5, 2, and 1.5 angstrom= > s, etc.

I'd prefer the 2nd way, which re= > quires more computational time but can have all other geometric parameters = > (except for the distance between H2 and Fe) optimized.
t>
face=3D"Calibri,Arial,Helvetica,sans-serif" color=3D"black">
argin-top:0px;margin-bottom:0px">Sincerely,
> >
>
Yingbin
> >
>
>

> >
>
>Yingbin Ge, Associate Professor
> > Science Building 207A
> > Department of Chemistry
> > Central Washington University
> > 400 E University Way
> > Ellensburg, WA 98926
> > Office Phone: 509-963-2817
 r>

On Fri, M= > ar 20, 2015 at 7:16 AM, Safiya Ess Amer amersaf85|,| .com">yahoo.com < _+_ccl.net" target=3D"_blank">owner-chemistry_+_ccl.net> wrote: r>
1px #ccc solid;padding-left:1ex">
> Sent to CCL by: "Safiya Ess Amer" [amersaf85!=3D! //yahoo.com" target=3D"_blank">yahoo.com]
> Hello for all
> I am using G03W to get results of a system H2-Fe(OH)3. I want to change the= >
> positions of two hydrogen atoms in Z direction and get energy at each posit= > ion.
> How can I use scan keyword to move more than one atom at the same time (as = > two
> hydrogen atoms mentioned above).
>
> Thanks in advance
>
> Safiya Amer
> amersaf85_-_yaho= > o.com
>
>
>
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> > --001a114232f26583720511bba79d-- > > Thank you to reply Assoc Prof Yingbin. I thought about using dummy atom at center of H2 molecule but I couldn't. I don't know ghost atom, is it same a dummy atom? I frozen all atoms of the system at suitable coordinates and ran program to get energy as you said in the 2nd way, but without using dummy atom. The positions of H2 atoms changed manually each time. I need a way with automaticaly changing for positions. in other words, scaning of more than one atom automatically rather than manually. have a nice day