From owner-chemistry@ccl.net Wed Jul 6 06:49:00 2011 From: "Eliac Brown Eliacbrown _ yahoo.com" To: CCL Subject: CCL: Scan - BSSE Message-Id: <-45029-110706064738-14308-6iwh+f173ZkDPSgDAFHvvQ##server.ccl.net> X-Original-From: "Eliac Brown" Date: Wed, 6 Jul 2011 06:47:36 -0400 Sent to CCL by: "Eliac Brown" [Eliacbrown[]yahoo.com] Dear All I am running an optimization job, followed by rigid PES scan. In the energy calculation, we are going to take BSSE into account. But what's about Scan? how can I add BSSE option into PES. Can I calculate the BSSE for the optimized structure and then added the calculated BSSE to all the scanned energies? I have also one more question, during the scan I found more stable configurations, but when I took the most stable configurations and optimized it, I found it is not stable and shifted to a weird configurations. BTW the the energy difference between the start optimized structure and the most stable configuration (got throughout the scan job) is around 2 kcal/mol. Any explanation for this shift? Any kind of help would be highly appreciated. Thanks Eliac From owner-chemistry@ccl.net Wed Jul 6 08:59:00 2011 From: "goska malgorzata.biczysko]=[sns.it" To: CCL Subject: CCL: G09: vibrationally resolved absorption spectra in G09 Message-Id: <-45030-110706064406-29339-kE6HsFgQB4BnX5brtgHYUA,server.ccl.net> X-Original-From: "goska" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 6 Jul 2011 12:43:56 +0200 MIME-Version: 1.0 Sent to CCL by: "goska" [malgorzata.biczysko.:.sns.it] Please take a look at http://idea.sns.it/files/idea/docs/vibronic_spectra_G09-A02.pdf for some technical hints, regards Malgorzata ----- Original Message ----- > From: "Saman mandegar mandegar_saman]=[yahoo.com" To: "Biczysko, Goska " Sent: Tuesday, July 05, 2011 9:50 PM Subject: CCL: G09: vibrationally resolved absorption spectra in G09 > > Sent to CCL by: "Saman mandegar" [mandegar_saman[#]yahoo.com] > Dear All, > > I am trying to compute the vibrationally resolved absorption and emission > spectra of some dyes. I am trying to utilize G09 for this goal. I am > wondering > to ask some technical and practical issues regarding the current > development. I > would be very grateful if I can set contact for discussion with someone > who is > experienced in this field. > Best regards, > Saman> > From owner-chemistry@ccl.net Wed Jul 6 09:55:01 2011 From: "Bernd Doser doser/./avmatsim.de" To: CCL Subject: CCL: Scan - BSSE Message-Id: <-45031-110706094823-25411-efWVekov71UsoLxUOfwrGw]~[server.ccl.net> X-Original-From: Bernd Doser Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 06 Jul 2011 15:48:14 +0200 MIME-Version: 1.0 Sent to CCL by: Bernd Doser [doser/./avmatsim.de] Dear Eliac, the BSSE strongly depends on the molecular structure. To correct a PES scan you have to do the BSSE correction for every single point. Therefore, it is not possible to use the BSSE correction of the optimized structure for the correction of other structures. This also will explain your other two observations. The optimized structure is on a BSSE corrected PES, whereas your PES scan is not BSSE corrected. So you compare two different things, which leads to large differences in energies and structures. All the best, Bernd On 06.07.2011 12:47, Eliac Brown Eliacbrown _ yahoo.com wrote: > Sent to CCL by: "Eliac Brown" [Eliacbrown[]yahoo.com] > Dear All > I am running an optimization job, followed by rigid PES scan. > In the energy calculation, we are going to take BSSE into account. > But what's about Scan? how can I add BSSE option into PES. > Can I calculate the BSSE for the optimized structure and then added the > calculated BSSE to all the scanned energies? > I have also one more question, during the scan I found more stable > configurations, but when I took the most stable configurations and optimized > it, I found it is not stable and shifted to a weird configurations. BTW the the > energy difference between the start optimized structure and the most stable > configuration (got throughout the scan job) is around 2 kcal/mol. Any > explanation for this shift? > Any kind of help would be highly appreciated. > Thanks Eliac> > > -- Dr Bernd Doser Scientific Software Engineer Avant-garde Materials Simulation Merzhauser Strasse 177 79100 Freiburg im Breisgau, Germany Phone: +49 761 479984-23 Homepage: http://www.avmatsim.de From owner-chemistry@ccl.net Wed Jul 6 10:29:00 2011 From: "Gegham Galstyan gegham(a)chemie.fu-berlin.de" To: CCL Subject: CCL:G: How to visualize molecular orbitals from Gaussian09 output file? Message-Id: <-45032-110706094622-22536-Ar+5wkegaBH8qwMO+FLgoA:+:server.ccl.net> X-Original-From: "Gegham Galstyan" Date: Wed, 6 Jul 2011 09:46:20 -0400 Sent to CCL by: "Gegham Galstyan" [gegham%%chemie.fu-berlin.de] Dear CCLers, do you know any good software for linux, mac or windows that can be used to visualize occupied molecular orbitals from gaussian03 output? I just want to quickly select the occupied pi-MOs among all MOs in a given molecule. Thanks a lot beforehand for any help/suggestion. With best wishes, Gegham -- Gegham Galstyan PhD student at AG Knapp Macromolecular Modeling Group Institute for Chemistry and Biochemistry Free University of Berlin Fabeckstr. 36a, 14195 Berlin, Germany Tel. +49 30 838 53612 e-mail: gegham^^^chemie.fu-berlin.de From owner-chemistry@ccl.net Wed Jul 6 11:04:00 2011 From: "Gegham Galstyan gegham/a\zedat.fu-berlin.de" To: CCL Subject: CCL:G: How to visualize molecular orbitals from Gaussian output file? Message-Id: <-45033-110706094844-25660-eJ9s/Mp8/sWLLLm7VN7KNw_-_server.ccl.net> X-Original-From: Gegham Galstyan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 06 Jul 2011 15:48:36 +0200 MIME-Version: 1.0 Sent to CCL by: Gegham Galstyan [gegham[]zedat.fu-berlin.de] Dear CCLers, do you know any good software for linux, mac or windows that can be used to visualize occupied molecular orbitals from gaussian03 output? I just want to quickly select the occupied pi-MOs among all MOs in a given molecule. Thanks a lot beforehand for any help/suggestion. With best wishes, Gegham --- Gegham Galstyan PhD student at AG Knapp Macromolecular Modeling Group Institute for Chemistry and Biochemistry Free University of Berlin Fabeckstr. 36a, 14195 Berlin, Germany Tel. +49 30 838 53612 e-mail: gegham*chemie.fu-berlin.de From owner-chemistry@ccl.net Wed Jul 6 11:39:00 2011 From: "JL jeffrey.lebowski{}gmx.de" To: CCL Subject: CCL:G: AW: G: How to visualize molecular orbitals from Gaussian09 output file? Message-Id: <-45034-110706112425-24912-em5pTxP4vAx7vF19ejgd+A_-_server.ccl.net> X-Original-From: "JL" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 6 Jul 2011 17:24:07 +0200 MIME-Version: 1.0 Sent to CCL by: "JL" [jeffrey.lebowski/./gmx.de] chk or fchk file in "GaussView" which is provided by Gaussian Inc output/log file with "Molden" (therefore you need to put "#P GFINPUT IOP(6/7=3)" in the inputfile so that the outputfile contains all informations needed by Molden) -----Ursprüngliche Nachricht----- Von: owner-chemistry+jeffrey.lebowski==gmx.de*_*ccl.net [mailto:owner-chemistry+jeffrey.lebowski==gmx.de*_*ccl.net] Im Auftrag von Gegham Galstyan gegham(a)chemie.fu-berlin.de Gesendet: Mittwoch, 6. Juli 2011 15:46 An: Doe, John Betreff: CCL:G: How to visualize molecular orbitals from Gaussian09 output file? Sent to CCL by: "Gegham Galstyan" [gegham%%chemie.fu-berlin.de] Dear CCLers, do you know any good software for linux, mac or windows that can be used to visualize occupied molecular orbitals from gaussian03 output? I just want to quickly select the occupied pi-MOs among all MOs in a given molecule. Thanks a lot beforehand for any help/suggestion. With best wishes, Gegham -- Gegham Galstyan PhD student at AG Knapp Macromolecular Modeling Group Institute for Chemistry and Biochemistry Free University of Berlin Fabeckstr. 36a, 14195 Berlin, Germany Tel. +49 30 838 53612 e-mail: gegham- -chemie.fu-berlin.dehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Jul 6 12:14:00 2011 From: "dipankar roy theodip*gmail.com" To: CCL Subject: CCL:G: How to visualize molecular orbitals from Gaussian09 output file? Message-Id: <-45035-110706105845-31658-FlOevUwrK3zxa4R+Ew/+vw(_)server.ccl.net> X-Original-From: dipankar roy Content-Type: multipart/alternative; boundary=485b3979d9b6cae03304a767d57a Date: Wed, 6 Jul 2011 10:58:37 -0400 MIME-Version: 1.0 Sent to CCL by: dipankar roy [theodip]*[gmail.com] --485b3979d9b6cae03304a767d57a Content-Type: text/plain; charset=ISO-8859-1 Hi, You can try MOLDEN or MOLKEL. They are available freely. best, Dipankar Roy On Wed, Jul 6, 2011 at 9:46 AM, Gegham Galstyan gegham(a)chemie.fu-berlin.de wrote: > > Sent to CCL by: "Gegham Galstyan" [gegham%%chemie.fu-berlin.de] > > Dear CCLers, > > do you know any good software for linux, mac or windows that can be used to > visualize occupied molecular orbitals from gaussian03 output? I just want to > quickly select the occupied pi-MOs among all MOs in a given molecule. > Thanks a lot beforehand for any help/suggestion. > > With best wishes, > Gegham > > -- > Gegham Galstyan > PhD student at AG Knapp > Macromolecular Modeling Group > Institute for Chemistry and Biochemistry > Free University of Berlin > Fabeckstr. 36a, 14195 Berlin, Germany > Tel. +49 30 838 53612 > e-mail: gegham- -chemie.fu-berlin.de> > > -- ----------------------------------- Dr. Dipankar Roy Research Associate Hunter College (CUNY) 695 Park Avenue New York, USA NY-10065 ----------------------------------- --485b3979d9b6cae03304a767d57a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
You can try MOLDEN or MOLKEL. They are available freely.
=
best,
Dipankar Roy

On Wed, Jul 6, 2011 at 9:46 AM, Gegham Galstyan gegham(a)chemie.fu-berlin.de <owner-chemistry!A!ccl.net> wrote:

Sent to CCL by: "Gegham =A0Galstyan" [gegham%%chemie.fu-berlin.de]

Dear CCLers,

do you know any good software for linux, mac or windows that can be used to= visualize occupied molecular orbitals from gaussian03 output? I just want = to quickly select the occupied pi-MOs among all MOs in a given molecule. Thanks a lot beforehand for any help/suggestion.

With best wishes,
Gegham

--
Gegham Galstyan
PhD student at AG Knapp
Macromolecular Modeling Group
Institute for Chemistry and Biochemistry
Free University of Berlin
Fabeckstr. 36a, 14195 Berlin, Germany
Tel. +49 3= 0 838 53612
e-mail: gegham- -c= hemie.fu-berlin.de



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY!A!ccl.n= et or use:
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--
-----------------------= ------------
Dr. Dipankar Roy
Research Associate
Hu= nter College (CUNY)
695 Park Avenue
New York, USA
NY-10065
-----------------------------------

--485b3979d9b6cae03304a767d57a-- From owner-chemistry@ccl.net Wed Jul 6 13:17:00 2011 From: "=?ISO-8859-1?Q?Francisco_Nu=F1ez_Za?=rur fnunez*_*klingon.uab.es" To: CCL Subject: CCL:G: How to visualize molecular orbitals from Gaussian output file? Message-Id: <-45036-110706121020-7379-yMqKILkVlE6HL8yvVutMMA-x-server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Francisco_Nu=F1ez_Za?=rur Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Wed, 06 Jul 2011 18:09:42 +0200 MIME-version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Francisco_Nu=F1ez_Za?=rur [fnunez+/-klingon.uab.es] Dear Gegham, if you are a Guassian user, you probably have the GaussView utility software. This web: http://gaussian.com/g_tech/gv5ref/results.htm#surface provides a very easy tutorial for your purposes. Another softwares you can use are Molden or ChemCraft. Good luck !! Francisco Nuñez Zarur Unidad de Química-Física Edificio C, C7-149 Departamento de Química Universidad Autónoma de Barcelona Bellaterra 08193. España Tel: +34 93 581 2173 Fax: +34 93 581 2920 ---------- Original Message ----------- > From: "Gegham Galstyan gegham/azedat.fu-berlin.de" To: "Nunez Zarur, Francisco " Sent: Wed, 06 Jul 2011 15:48:36 +0200 Subject: CCL:G: How to visualize molecular orbitals from Gaussian output file? > Sent to CCL by: Gegham Galstyan [gegham[]zedat.fu-berlin.de] > Dear CCLers, > > do you know any good software for linux, mac or windows that can be used to visualize occupied molecular orbitals from gaussian03 output? I just want to quickly select the occupied pi-MOs among all MOs in a given molecule. > Thanks a lot beforehand for any help/suggestion. > > With best wishes, > Gegham > > --- > Gegham Galstyan > PhD student at AG Knapp > Macromolecular Modeling Group > Institute for Chemistry and Biochemistry > Free University of Berlin > Fabeckstr. 36a, 14195 Berlin, Germany > Tel. +49 30 838 53612 > e-mail: gegham:+:chemie.fu-berlin.de------- End of Original Message ------- From owner-chemistry@ccl.net Wed Jul 6 13:52:00 2011 From: "=?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= gjgarcia- -ujaen.es" To: CCL Subject: CCL:G: How to visualize molecular orbitals from Gaussian output file? Message-Id: <-45037-110706120424-852-Q1QY/E7gpHW5oeWuhqNlKw[a]server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 06 Jul 2011 18:04:06 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Gregorio_Garc=EDa_Moreno?= [gjgarcia++ujaen.es] Hi You can visualize molecular orbitals with gausview from fchk file. El 7/6/2011 3:48 PM, Gegham Galstyan gegham/azedat.fu-berlin.de escribió: > > Sent to CCL by: Gegham Galstyan [gegham[]zedat.fu-berlin.de] > Dear CCLers, > > do you know any good software for linux, mac or windows that can be > used to visualize occupied molecular orbitals from gaussian03 output? > I just want to quickly select the occupied pi-MOs among all MOs in a > given molecule. > Thanks a lot beforehand for any help/suggestion. > > With best wishes, > Gegham > > --- > Gegham Galstyan > PhD student at AG Knapp > Macromolecular Modeling Group > Institute for Chemistry and Biochemistry > Free University of Berlin > Fabeckstr. 36a, 14195 Berlin, Germany > Tel. +49 30 838 53612 > e-mail: gegham:+:chemie.fu-berlin.dehttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Gregorio García Moreno PhD student Department of Physical and Analytical Chemistry University of Jaén From owner-chemistry@ccl.net Wed Jul 6 14:27:00 2011 From: "Benjamin Stein benjamin.w.stein[a]gmail.com" To: CCL Subject: CCL:G: How to visualize molecular orbitals from Gaussian output file? Message-Id: <-45038-110706122553-22375-3Bjxq7+2oPwdyOjhL1hcBA-$-server.ccl.net> X-Original-From: Benjamin Stein Content-Type: multipart/alternative; boundary=Apple-Mail-7-949837321 Date: Wed, 6 Jul 2011 10:25:18 -0600 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Benjamin Stein [benjamin.w.stein[A]gmail.com] --Apple-Mail-7-949837321 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Avogadro (http://avogadro.openmolecules.net/) works well, and is free. = Simply open a formatted checkpoint file and you're ready to go. It also = works on all three platforms. On Jul 6, 2011, at 7:48 AM, Gegham Galstyan gegham/azedat.fu-berlin.de = wrote: >=20 > Sent to CCL by: Gegham Galstyan [gegham[]zedat.fu-berlin.de] > Dear CCLers, >=20 > do you know any good software for linux, mac or windows that can be = used to visualize occupied molecular orbitals from gaussian03 output? I = just want to quickly select the occupied pi-MOs among all MOs in a given = molecule. > Thanks a lot beforehand for any help/suggestion. >=20 > With best wishes, > Gegham >=20 > --- > Gegham Galstyan > PhD student at AG Knapp > Macromolecular Modeling Group > Institute for Chemistry and Biochemistry > Free University of Berlin > Fabeckstr. 36a, 14195 Berlin, Germany > Tel. +49 30 838 53612 > e-mail: gegham:+:chemie.fu-berlin.de >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20=>=20>=20Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail-7-949837321 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii http://avogadro.openmolecules.= net/) works well, and is free. Simply open a formatted checkpoint = file and you're ready to go. It also works on all three = platforms.

On Jul 6, 2011, at 7:48 AM, Gegham Galstyan = gegham/azedat.fu-berlin.de wrote:


Sent to CCL by: Gegham Galstyan = [gegham[]zedat.fu-berlin.de]
Dear CCLers,

do you know any good = software for linux, mac or windows that can be used to visualize = occupied molecular orbitals from gaussian03 output? I just want to = quickly select the occupied pi-MOs among all MOs in a given = molecule.
Thanks a lot beforehand for any = help/suggestion.

With best wishes,
Gegham

---
Gegham = Galstyan
PhD student at AG Knapp
Macromolecular Modeling = Group
Institute for Chemistry and Biochemistry
Free University of = Berlin
Fabeckstr. 36a, 14195 Berlin, Germany
Tel. +49 30 838 = 53612
e-mail: gegham:+:chemie.fu-berlin.de


-=3D This is automatically added to each message by the mailing script = =3D-
To recover the email address of the author of the message, = please change
the strange characters on the top line to the /./ sign. = You can also
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Before posting, check wait time at: = http://www.ccl.net

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<= /div>
= --Apple-Mail-7-949837321-- From owner-chemistry@ccl.net Wed Jul 6 15:02:00 2011 From: "Osvaldo Gutierrez ogutierrez,ucdavis.edu" To: CCL Subject: CCL:G: How to visualize molecular orbitals from Gaussian09 output file? Message-Id: <-45039-110706120130-30436-6EqsngVLsLFsrJAkf4dZRw!A!server.ccl.net> X-Original-From: Osvaldo Gutierrez Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 6 Jul 2011 09:01:23 -0700 MIME-Version: 1.0 Sent to CCL by: Osvaldo Gutierrez [ogutierrez,ucdavis.edu] Dear Gehham, Molekel software is free and it's a decent program that will allow you to accomplish your task. Osvaldo On Wednesday, July 6, 2011, Gegham Galstyan gegham(a)chemie.fu-berlin.de wrote: > > Sent to CCL by: "Gegham  Galstyan" [gegham%%chemie.fu-berlin.de] > > Dear CCLers, > > do you know any good software for linux, mac or windows that can be used to visualize occupied molecular orbitals from gaussian03 output? I just want to quickly select the occupied pi-MOs among all MOs in a given molecule. > Thanks a lot beforehand for any help/suggestion. > > With best wishes, > Gegham > > -- > Gegham Galstyan > PhD student at AG Knapp > Macromolecular Modeling Group > Institute for Chemistry and Biochemistry > Free University of Berlin > Fabeckstr. 36a, 14195 Berlin, Germany > Tel. +49 30 838 53612 > e-mail: gegham- -chemie.fu-berlin.de > > > >>>>> >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message > >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message > >>      http://www.ccl.net/chemistry/sub_unsub.shtml > >> >>> >> >>      http://www.ccl.net/spammers.txt > >> > > -- Osvaldo Gutierrez UC Davis Chemistry 310-990-5289 From owner-chemistry@ccl.net Wed Jul 6 17:01:00 2011 From: "Ol Ga eurisco1]=[pochta.ru" To: CCL Subject: CCL: How to visualize molecular orbitals from Gaussian output file? Message-Id: <-45040-110706144042-23569-rXia8BH+rVdq9qlwJXAGtQ:+:server.ccl.net> X-Original-From: "Ol Ga" Date: Wed, 6 Jul 2011 14:40:39 -0400 Sent to CCL by: "Ol Ga" [eurisco1^pochta.ru] Dear Gegham Galstyan, ChemCraft can read and visualize orbitals. Just group "gfinput POP=FULL" is required. Sincerely, Ol Ga From owner-chemistry@ccl.net Wed Jul 6 22:49:00 2011 From: "Eli Lam elizabeth.shlam-#-gmail.com" To: CCL Subject: CCL: SCF Done Difference in pop(full) and TDDFT Message-Id: <-45041-110706224752-27968-uRlgOZSmmZU8pBEASO4SAQ#%#server.ccl.net> X-Original-From: "Eli Lam" Date: Wed, 6 Jul 2011 22:47:47 -0400 Sent to CCL by: "Eli Lam" [elizabeth.shlam[]gmail.com] Hi CCLers, I've just spotted there is always a difference in the SCF energy between the job pop(full) and TDDFT. Is it normal? If yes, why is that so? If not, how could I solve the problem? The route are as followed: For pop(full) job: #n PBE1PBE gen pop(full) pseudo=read SCRF(CPCM,Solvent=Dichloromethane ) GFINPUT IOP(3/33=1) 5D 7F Geom=check For TDDFT job: #n PBE1PBE TD(NStates=5) gen pseudo=read SCRF(CPCM,Solvent=Dichlorome thane) GFINPUT IOP(6/7=3) 5D 7F Geom=check Thanks so much! Eli