From owner-chemistry@ccl.net Thu Apr 8 05:32:00 2010 From: "Jens Spanget-Larsen spanget~!~ruc.dk" To: CCL Subject: CCL:G: 3d Orbtial using Gaussian Message-Id: <-41618-100408044753-21923-w/8woSZc9t4otrb+srIBSQ*o*server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 08 Apr 2010 10:18:05 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget]_[ruc.dk] Dear Decai Yu, the keywords 5D and 6D specify use of either the five so-called "pure d" basis functions or the six second order functions. Similarly for the f shell, 7F or 10F. Consult the manual concerning pure vs. Cartesian basis functions. Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget:-:ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Decai Yu decai-yu%a%northwestern.edu wrote: > Sent to CCL by: "Decai Yu" [decai-yu[A]northwestern.edu] > Dear All, > > In the Gaussian calculations, the d orbitals look like XX, YY, ZZ, XY, > XZ, YZ. How do I convert them into the 5 independent d orbitals (XY, > XZ,YZ,X2-Y2, > Z2)? I would appreciate any help on this. > > Regards, > > Decai Yu> > > From owner-chemistry@ccl.net Thu Apr 8 06:06:00 2010 From: "Georg Lefkidis lefkidis:-:physik.uni-kl.de" To: CCL Subject: CCL:G: AW: G: 3d Orbtial using Gaussian Message-Id: <-41619-100408032714-25911-bCIx+G3ltLy1bhp6NBoEIA*|*server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Language: de Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 8 Apr 2010 08:57:01 +0200 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis%x%physik.uni-kl.de] Dear Decai Yu, rerun the calculation with the 5D option (simply add it in the command = line) Cheers George -----Urspr=FCngliche Nachricht----- Von: owner-chemistry+lefkidis=3D=3Dphysik.uni-kl.de#,#ccl.net [mailto:owner-chemistry+lefkidis=3D=3Dphysik.uni-kl.de#,#ccl.net] Im = Auftrag von Decai Yu decai-yu%a%northwestern.edu Gesendet: Donnerstag, 8. April 2010 00:09 An: Lefkidis, Georg Betreff: CCL:G: 3d Orbtial using Gaussian Sent to CCL by: "Decai Yu" [decai-yu[A]northwestern.edu] Dear All, =20 In the Gaussian calculations, the d orbitals look like XX, YY, ZZ, XY, XZ, YZ. How do I convert them into the 5 independent d orbitals (XY, XZ,YZ,X2-Y2, Z2)? I would appreciate any help on this. =20 Regards, =20 Decai Yu ------------------------------------------------------------------- Dr. Georg Lefkidis Dept. of Physics University of Kaiserslautern PO Box 3049 67653 Kaiserslautern e-mail: lefkidis(at)physik(dot)uni(dash)kl(dot)de Tel.: +49 631 205 3207 ------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Apr 8 08:22:01 2010 From: "W. Flak williamflak,+,yahoo.com" To: CCL Subject: CCL:G: MM optimization Message-Id: <-41620-100408060211-6817-o6y9jcC1sMRAo7EVtgSwXA * server.ccl.net> X-Original-From: "W. Flak" Date: Thu, 8 Apr 2010 06:02:10 -0400 Sent to CCL by: "W. Flak" [williamflak^^yahoo.com] Dear CCL users I tried to optimize two non bonded molecules using MM method (amber) inside gaussian. I found the distance between two molecules doesn't change, only each molecule (fragment) does optimize, even if the two molecules are so close to each other (0.1 A). According to MM, there is a non bonded interaction and depends on van der waals radius of the atoms. So, why the distance between the two molecules (even if amino acid residues) doesn't change? Is there a mistake in my trials? or I missed a concept? Any kind of help will be appreciated. thanks From owner-chemistry@ccl.net Thu Apr 8 14:17:00 2010 From: "Decai Yu decai-yu . northwestern.edu" To: CCL Subject: CCL:G: visualizing NBO using Molekel Message-Id: <-41621-100408133540-24924-1oayn+DcuXTPNn4vRaCnRg%%server.ccl.net> X-Original-From: "Decai Yu" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 8 Apr 2010 12:35:31 -0500 MIME-Version: 1.0 Sent to CCL by: "Decai Yu" [decai-yu#,#northwestern.edu] Dear All, I am trying to visualize NBO using Molekel. According to a previous post, http://www.ccl.net/chemistry/resources/messages/2007/04/05.011-dir/index .html I need to go to the menu load->nbo orb. But I couldn't find the "load" on the molekel 5.3. Any suggestions? Thanks! Decai Yu > -----Original Message----- > From: owner-chemistry+decai-yu==northwestern.edu(!)ccl.net [mailto:owner- > chemistry+decai-yu==northwestern.edu(!)ccl.net] On Behalf Of Jens Spanget- > Larsen spanget~!~ruc.dk > Sent: Thursday, April 08, 2010 3:18 AM > To: Yu, Decai > Subject: CCL:G: 3d Orbtial using Gaussian > > > Sent to CCL by: Jens Spanget-Larsen [spanget]_[ruc.dk] > > Dear Decai Yu, > the keywords 5D and 6D specify use of either the five so-called "pure d" > basis functions or the six second order functions. Similarly for the f > shell, 7F or 10F. Consult the manual concerning pure vs. Cartesian basis > functions. > Jens >--< > > ------------------------------------------------------ > JENS SPANGET-LARSEN Office: +45 4674 2710 > Dept. of Science (18.1) Fax: +45 4674 3011 > Roskilde University Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget() ruc.dk > DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget > ------------------------------------------------------ > > > > Decai Yu decai-yu%a%northwestern.edu wrote: > > Sent to CCL by: "Decai Yu" [decai-yu[A]northwestern.edu] > > Dear All, > > > > In the Gaussian calculations, the d orbitals look like XX, YY, ZZ, XY, > > XZ, YZ. How do I convert them into the 5 independent d orbitals (XY, > > XZ,YZ,X2-Y2, > > Z2)? I would appreciate any help on this. > > > > Regards, > > > > Decai Yu From owner-chemistry@ccl.net Thu Apr 8 16:10:00 2010 From: "Amir Taghavi amir_taghavi14,yahoo.com" To: CCL Subject: CCL:G: MM optimization Message-Id: <-41622-100408123634-12964-vwfZl1HNQJqJYsgQ95bsMA/./server.ccl.net> X-Original-From: Amir Taghavi Content-Type: multipart/alternative; boundary="0-505133581-1270744584=:69781" Date: Thu, 8 Apr 2010 09:36:24 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Amir Taghavi [amir_taghavi14~!~yahoo.com] --0-505133581-1270744584=:69781 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi,I suggest to you that you can do this job very easily through using a mo= lecular dynamics package, as many MD softwares do this MM optimizations tha= t change the whole configuration of system. If you name your molecules it w= ould be better.Hope this is helpful.Best regards,Amir=A0 --- On Thu, 4/8/10, W. Flak williamflak,+,yahoo.com wrote: > From: W. Flak williamflak,+,yahoo.com Subject: CCL:G: MM optimization To: "Taghavi, Amir " Date: Thursday, April 8, 2010, 10:02 AM Sent to CCL by: "W.=A0 Flak" [williamflak^^yahoo.com] Dear CCL users I tried to optimize two non bonded molecules using MM method (amber) inside= =20 gaussian. I found the distance between two molecules doesn't change, only e= ach=20 molecule (fragment) does optimize, even if the two molecules are so close t= o=20 each other (0.1 A). According to MM, there is a non bonded interaction and= =20 depends on van der waals radius of the atoms. So, why the distance between = the=20 two molecules (even if amino acid residues) doesn't change? Is there a mistake in my trials? or I missed a concept? Any kind of help will be appreciated. thanks -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-505133581-1270744584=:69781 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Hi,

I suggest to you that you ca= n do this job very easily through using a molecular dynamics package, as ma= ny MD softwares do this MM optimizations that change the whole configuratio= n of system. If you name your molecules it would be better.

Hope this= is helpful.

Best regards,

Amir=A0

--- On Thu, 4/8/10= , W. Flak williamflak,+,yahoo.com <owner-chemistry^^^ccl.net> wrote:

From: W. Flak williamflak,+,yahoo.= com <owner-chemistry^^^ccl.net>
Subject: CCL:G: MM optimization
T= o: "Taghavi, Amir " <amir_taghavi14^^^yahoo.com>
Date: Thurs= day, April 8, 2010, 10:02 AM


Sent to CC= L by: "W.=A0 Flak" [williamflak^^yahoo.com]
Dear CCL users
I tried to= optimize two non bonded molecules using MM method (amber) inside
gaussian. I fo= und the distance between two molecules doesn't change, only each
molecu= le (fragment) does optimize, even if the two molecules are so close to
= each other (0.1 A). According to MM, there is a non bonded interaction and =
depends on van der waals radius of the atoms. So, why the distance betw= een the
two molecules (even if amino acid residues) doesn't change?
= Is there a mistake in my trials? or I missed a concept?
Any kind of help= will be appreciated.
thanks



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=0A=0A --0-505133581-1270744584=:69781-- From owner-chemistry@ccl.net Thu Apr 8 16:50:01 2010 From: "Radoslaw Kaminski rkaminski.rk!=!gmail.com" To: CCL Subject: CCL:G: visualizing NBO using Molekel Message-Id: <-41623-100408164917-24329-wIt+MJArtDZOy/rZCx+OLA-$-server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=000e0ce0457c5121010483bfcf2b Date: Thu, 8 Apr 2010 16:49:06 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk a gmail.com] --000e0ce0457c5121010483bfcf2b Content-Type: text/plain; charset=ISO-8859-1 Hi, "But I couldn't find the "load" on the molekel 5.3." There is no any. You have to use Molekel 4.x to do that! Hope that helps. Radek 2010/4/8 Decai Yu decai-yu . northwestern.edu > > Sent to CCL by: "Decai Yu" [decai-yu#,#northwestern.edu] > Dear All, > > I am trying to visualize NBO using Molekel. > According to a previous post, > http://www.ccl.net/chemistry/resources/messages/2007/04/05.011-dir/index > .html > I need to go to the menu load->nbo orb. > But I couldn't find the "load" on the molekel 5.3. > Any suggestions? > > Thanks! > > Decai Yu > > > > > -----Original Message----- > > From: owner-chemistry+decai-yu==northwestern.edu() ccl.net > [mailto:owner- > > chemistry+decai-yu==northwestern.edu() ccl.net] On Behalf Of Jens > Spanget- > > Larsen spanget~!~ruc.dk > > Sent: Thursday, April 08, 2010 3:18 AM > > To: Yu, Decai > > Subject: CCL:G: 3d Orbtial using Gaussian > > > > > > Sent to CCL by: Jens Spanget-Larsen [spanget]_[ruc.dk] > > > > Dear Decai Yu, > > the keywords 5D and 6D specify use of either the five so-called "pure > d" > > basis functions or the six second order functions. Similarly for the f > > shell, 7F or 10F. Consult the manual concerning pure vs. Cartesian > basis > > functions. > > Jens >--< > > > > ------------------------------------------------------ > > JENS SPANGET-LARSEN Office: +45 4674 2710 > > Dept. of Science (18.1) Fax: +45 4674 3011 > > Roskilde University Mobile: +45 2320 6246 > > P.O.Box 260 E-Mail: spanget() ruc.dk > > DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget > > ------------------------------------------------------ > > > > > > > > Decai Yu decai-yu%a%northwestern.edu wrote: > > > Sent to CCL by: "Decai Yu" [decai-yu[A]northwestern.edu] > > > Dear All, > > > > > > In the Gaussian calculations, the d orbitals look like XX, YY, ZZ, > XY, > > > XZ, YZ. How do I convert them into the 5 independent d orbitals (XY, > > > XZ,YZ,X2-Y2, > > > Z2)? I would appreciate any help on this. > > > > > > Regards, > > > > > > Decai Yu> > > --000e0ce0457c5121010483bfcf2b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

"But I couldn't find the "load" on the moleke= l 5.3."

There is no any. You have to use Molekel 4.x to do that= !

Hope that helps.

Radek


2010/4/8 Decai Yu decai-yu . northweste= rn.edu <owner-chemistry() ccl.net>

Sent to CCL by: "Decai Yu" [decai-yu#,#northwestern.edu]
Dear All,

I am trying to visualize NBO using Molekel.
According to a previous post,
http://www.ccl.net/chemistry/resources/= messages/2007/04/05.011-dir/index
.html
I need to go to the menu load->nbo orb.
But I couldn't find the "load" on the molekel 5.3.
Any suggestions?

Thanks!

Decai Yu



> -----Original Message-----
> From: owner-chemistry+decai-yu=3D=3Dnorthwestern.edu() ccl.net
[mailto:owner-
> chemistry+decai-yu=3D=3Dnorthwestern.edu() ccl.net] On Behalf Of Jens
Spanget-
> Larsen spanget~!~ruc.dk
> Sent: Thursday, April 08, 2010 3:18 AM
> To: Yu, Decai
> Subject: CCL:G: 3d Orbtial using Gaussian
>
>
> Sent to CCL by: Jens Spanget-Larsen [spanget]_[ruc.dk]
>
> Dear Decai Yu,
> the keywords 5D and 6D specify use of either the five so-called "= pure
d"
> basis functions or the six second order functions. Similarly for the f=
> shell, 7F or 10F. Consult the manual concerning pure vs. Cartesian
basis
> functions.
> Jens >--<
>
> =A0 ------------------------------------------------------
> =A0 JENS SPANGET-LARSEN =A0 =A0 =A0 =A0 Office: =A0 =A0 =A0+45 4674 27= 10
> =A0 Dept. of Science (18.1) =A0 =A0 Fax: =A0 =A0 =A0 =A0 +45 4674 3011=
> =A0 Roskilde University =A0 =A0 =A0 =A0 Mobile: =A0 =A0 =A0+45 2320 62= 46
> =A0 P.O.Box 260 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 E-Mail: =A0 =A0 spange= t() ruc.dk
> =A0 DK-4000 Roskilde, Denmark =A0 http://www.ruc.dk/~spanget
> =A0 ------------------------------------------------------
>
>
>
> Decai Yu decai-yu%a%northwestern.edu wrote:
> > Sent to CCL by: "Decai Yu" [decai-yu[A]northwestern.edu]
> > Dear All,
> >
> > In the Gaussian calculations, the d orbitals look like XX, YY, ZZ= ,
XY,
> > XZ, YZ. How do I convert them into the 5 independent d orbitals (= XY,
> > XZ,YZ,X2-Y2,
> > =A0Z2)? I would appreciate any help on this.
> >
> > Regards,
> >
> > Decai Yu


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--000e0ce0457c5121010483bfcf2b-- From owner-chemistry@ccl.net Thu Apr 8 17:25:01 2010 From: "Mike F Falcetta mffalcetta-x-gcc.edu" To: CCL Subject: CCL:G: TDDFT in gaussian 09 Message-Id: <-41624-100408160809-28554-z3lSiQOT11UlH+jNO7t6RA(~)server.ccl.net> X-Original-From: "Mike F Falcetta" Date: Thu, 8 Apr 2010 16:08:08 -0400 Sent to CCL by: "Mike F Falcetta" [mffalcetta * gcc.edu] I am running some trial TDDFT calculations with gaussian 09 using the b2plyp and wB97xD functionals. My question is which parts of these functionals actually affect the excitation energies. My guess is that the long-range correction for the exchange does affect them but the dispersion correction in the wb97xD and and perturbative correlation corrections in b2bplyp do not. IF anyone can either confirm or correct my assumption and/or point me to a further discussion on the matter I woudl greatly appreciate it. Thanks in advance Mike From owner-chemistry@ccl.net Thu Apr 8 20:32:00 2010 From: "Neeraj Naithani neerajnaithani(~)gmail.com" To: CCL Subject: CCL: regarding molecular dynamics simulation Message-Id: <-41625-100407212250-4035-sGpDLK6s7hQEu9gfCShCAg#%#server.ccl.net> X-Original-From: "Neeraj Naithani" Date: Wed, 7 Apr 2010 21:22:49 -0400 Sent to CCL by: "Neeraj Naithani" [neerajnaithani+*+gmail.com] i am using acclrys material studio. i want to know that whether charged molecules can be taken for constructing a cell. i have tried but it is giving error. i am using compass force field