From owner-chemistry@ccl.net Wed Nov 4 00:02:01 2015 From: "Subrahmanyam Sappati subrahmanyamsappati . gmail.com" To: CCL Subject: CCL:G: DOS calculations with G09 Message-Id: <-51852-151104000022-13671-WH5Ot1LEgx23bcA5RJ0LNw^-^server.ccl.net> X-Original-From: Subrahmanyam Sappati Content-Type: multipart/alternative; boundary=001a113dfa5eea64860523afe224 Date: Wed, 4 Nov 2015 10:30:16 +0530 MIME-Version: 1.0 Sent to CCL by: Subrahmanyam Sappati [subrahmanyamsappati]~[gmail.com] --001a113dfa5eea64860523afe224 Content-Type: text/plain; charset=UTF-8 Hi, GaussSum software is the one of the tool to plot DOS. See the attached link. http://gausssum.sourceforge.net/Example/index.html Regards Subrahmanyam On Wed, Nov 4, 2015 at 4:11 AM, rayen mahi mahi.rayen-$-gmail.com < owner-chemistry^ccl.net> wrote: > Hello everyone, > > > Does anyone know how to get density of states with Gaussian09 ? I need > the command for the input file . > > > I appreciate your help > -- Subrahmanyam.Sappati C/o Dr. Prasenjit Ghosh IISER PUNE Pin code : 411 008 Phone : +91 94 03 59 35 18 --001a113dfa5eea64860523afe224 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,

GaussSum=C2=A0 software is the one of the tool to= plot DOS. See the attached link.

http://gausssum.sourceforge.net/Example/index.= html

Regards
Subrahmanyam


On Wed, Nov 4, 2015 a= t 4:11 AM, rayen mahi mahi.rayen-$-gmail.com <owner-chemistry^ccl.net> wrote:

Hello everyone,


Does any= one know how to get density of states wi= th Gaussian09 ? I need the command for the =C2= =A0input file .


I appreciate your help




--

Subrahmanyam.Sappati
C/o Dr. Prasenjit Ghosh
IISER PUNE
Pin code : 411 008

= Phone : +91 94 03 59 35 18=

--001a113dfa5eea64860523afe224-- From owner-chemistry@ccl.net Wed Nov 4 06:47:01 2015 From: "Ren Jiajun jiajunren0522^-^163.com" To: CCL Subject: CCL: molcas localisation module Message-Id: <-51853-151104035905-29259-DcE6WM/l24taNt8l4j/INQ%x%server.ccl.net> X-Original-From: "Ren Jiajun" Date: Wed, 4 Nov 2015 03:59:04 -0500 Sent to CCL by: "Ren Jiajun" [jiajunren0522|-|163.com] Hello, everyone Can someone tell me how to use localisation module to do localization in one specific irrep in occupied and virtual space respectively? it seems that CHOLesky method is used. best Regards, Jiajun From owner-chemistry@ccl.net Wed Nov 4 07:22:00 2015 From: "Petra Matunova petra.matunova]![seznam.cz" To: CCL Subject: CCL:G: ONIOM calculations in Gaussian Message-Id: <-51854-151104060624-12814-ni9WRYepUmChYWfkLaqFHw^^^server.ccl.net> X-Original-From: "Petra Matunova" Date: Wed, 4 Nov 2015 06:06:21 -0500 Sent to CCL by: "Petra Matunova" [petra.matunova%%seznam.cz] I am performing an ONIOM optimization calculation of a diamond nanoparticle, using b3lyp/6-31g(d):b3lyp/3-21g method. The system contains 206 C atoms and 130 H atoms in the high level and 488 C atoms 188 H atoms in the low level. When I set the charge and multiplicity as following: 0 1 0 1 0 1, the system do the low level SCF calculation without problems, but when starts with the high level calculation on the model system, it ends with error: The combination of multiplicity 1 and 1455 electrons is impossible. It only works when I set 0 1 0 2 0 2. In the high level system there are 1366 electrons plus 89 link electrons from H atoms used as link atoms. I had a problem with the specification of the link atoms on the boundary between the low level and high level system. The low level C atom close to the boundary has two bonds to another 2 high level C atoms. I haven't known how to deal with that, as far as I know Gaussian allows to specify only one bond to for every low level atom to a high level atom. So I specified for the low level C atom linked to 2 high level C atoms only one link H atom and set the corresponding scale factor to 1, e.g.: C -1 3.953927 3.329465 3.558583 L H 18 1. Like this, I got only a following warning in output, e.g.: WARNING: Link atom host 21 is close to both atoms 18 and 123. Should it be oligovalent? Is there a way how to specify a link of the low level C to both of the high level C to which it is bonded? Or how to solve that, would it be right to leave the multiplicity to one? Thank you for your help! Best regards, Petra From owner-chemistry@ccl.net Wed Nov 4 09:08:01 2015 From: "Tian Lu sobereva()sina.com" To: CCL Subject: CCL:G: DOS calculations with G09 Message-Id: <-51855-151104021410-22255-kj4ukyes7vJPH4kXa4d9LQ(-)server.ccl.net> X-Original-From: "Tian Lu" Date: Wed, 4 Nov 2015 02:14:07 -0500 Sent to CCL by: "Tian Lu" [sobereva]|[sina.com] Hi, If you are studying isolated systems, you can easily use main function 10 of Multiwfn program to plot TDOS, PDOS and OPDOS based on Gaussian .fch file. Examples can be found in Section 4.10 of the manual. -------------------------------- Best wishes, Tian Lu Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China ----- Original Message ----- > From: "rayen mahi mahi.rayen-$-gmail.com" To: "Lu, Tian " Subject: CCL:G: DOS calculations with G09 Date: 2015-11-04 07:27 Hello everyone, Does anyone know how to get density of states with Gaussian09 ? I need the command for the input file . I appreciate your help From owner-chemistry@ccl.net Wed Nov 4 11:52:01 2015 From: "rayen mahi mahi.rayen===gmail.com" To: CCL Subject: CCL:G: DOS calculations with G09 Message-Id: <-51856-151104114919-6398-6DsC0J2jTMrjqV0pAQGQDQ,server.ccl.net> X-Original-From: rayen mahi Content-Type: multipart/alternative; boundary=001a1138f8645b76720523b9ca41 Date: Wed, 4 Nov 2015 17:49:14 +0100 MIME-Version: 1.0 Sent to CCL by: rayen mahi [mahi.rayen(-)gmail.com] --001a1138f8645b76720523b9ca41 Content-Type: text/plain; charset=UTF-8 Thank you all for your help The system that I am working on is constituted by 2 fragments during the optimization of the structure I had to freeze the atoms that doesn't intervene in the interactions between the fragments. should I do the same thing during DOS calculation? 2015-11-04 8:14 GMT+01:00 Tian Lu sobereva()sina.com < owner-chemistry]~[ccl.net>: > > Sent to CCL by: "Tian Lu" [sobereva]|[sina.com] > Hi, > > If you are studying isolated systems, you can easily use main function 10 > of Multiwfn program to plot TDOS, PDOS and OPDOS based on Gaussian .fch > file. Examples can be found in Section 4.10 of the manual. > > -------------------------------- > > Best wishes, > > Tian Lu > Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China > > > ----- Original Message ----- > > From: "rayen mahi mahi.rayen-$-gmail.com" > To: "Lu, Tian " > Subject: CCL:G: DOS calculations with G09 > Date: 2015-11-04 07:27 > > Hello everyone, > > > Does anyone know how to get density of states with Gaussian09 ? I need the > command for the input file . > > > I appreciate your help> > > --001a1138f8645b76720523b9ca41 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thank you all for your help

= The system that I am working on is constituted by 2 fragments during the op= timization of the structure I had to freeze the atoms that doesn't inte= rvene in the interactions between the fragments. should =C2=A0I do the same= thing during DOS calculation?

2015-11-04 8:14 GMT+01:00 Tian Lu sobereva()sina.com <owner-chemistry]~[ccl.net><= /span>:

Sent to CCL by: "Tian=C2=A0 Lu" [sobereva]|[sina.com]
Hi,

If you are studying isolated systems, you can easily use main function 10 o= f Multiwfn program to plot TDOS, PDOS and OPDOS based on Gaussian .fch file= . Examples can be found in Section 4.10 of the manual.

--------------------------------

Best wishes,

Tian Lu
Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China


----- Original Message -----
> From: "rayen mahi mahi.rayen-$-gmail.com" <owner-chemistry(a= )ccl.net>
To: "Lu, Tian " <sobereva(a)sina.com>
Subject: CCL:G: DOS calculations with G09
Date: 2015-11-04 07:27

Hello everyone,


Does anyone know how to get density of states with Gaussian09 ? I need the = command for the=C2=A0 input file .


I appreciate your help



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--001a1138f8645b76720523b9ca41-- From owner-chemistry@ccl.net Wed Nov 4 12:26:00 2015 From: "zborowsk zborowsk[a]chemia.uj.edu.pl" To: CCL Subject: CCL:G: ONIOM calculations in Gaussian Message-Id: <-51857-151104115518-7957-2LiMi1fhhE2HPs4XHSHdww%a%server.ccl.net> X-Original-From: zborowsk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 04 Nov 2015 17:55:04 +0100 MIME-Version: 1.0 Sent to CCL by: zborowsk [zborowsk%chemia.uj.edu.pl] I must say I am a bit suprised by presence of hydrogen in your diamond.... W dniu 2015-11-04 12:06, Petra Matunova petra.matunova]![seznam.cz napisał(a): > Sent to CCL by: "Petra Matunova" [petra.matunova%%seznam.cz] > I am performing an ONIOM optimization calculation of a diamond > nanoparticle, using b3lyp/6-31g(d):b3lyp/3-21g method. The system > contains 206 C atoms and 130 H atoms in the high level and 488 C > atoms > 188 H atoms in the low level. When I set the charge and multiplicity > as following: 0 1 0 1 0 1, the system do the low level SCF > calculation > without problems, but when starts with the high level calculation on > the model system, it ends with error: > > The combination of multiplicity 1 and 1455 electrons is impossible. > > It only works when I set 0 1 0 2 0 2. In the high level system there > are 1366 electrons plus 89 link electrons from H atoms used as link > atoms. > > I had a problem with the specification of the link atoms on the > boundary between the low level and high level system. The low level C > atom close to the boundary has two bonds to another 2 high level C > atoms. I haven't known how to deal with that, as far as I know > Gaussian allows to specify only one bond to for every low level atom > to a high level atom. So I specified for the low level C atom linked > to 2 high level C atoms only one link H atom and set the > corresponding > scale factor to 1, e.g.: > > C -1 3.953927 3.329465 3.558583 L H 18 1. > > Like this, I got only a following warning in output, e.g.: > > WARNING: Link atom host 21 is close to both atoms 18 and 123. > Should it be oligovalent? > > Is there a way how to specify a link of the low level C to both of > the high level C to which it is bonded? Or how to solve that, would > it > be right to leave the multiplicity to one? > > Thank you for your help! > Best regards, > Petra > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/-- https://www.youtube.com/watch?v=IGyfx3Pmeyk Krzysztof K. Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)663-2067 email: zborowsk]~[chemia.uj.edu.pl gg 3817259 skype kzys70 www.chemia.uj.edu.pl/~zborowsk From owner-chemistry@ccl.net Wed Nov 4 22:24:00 2015 From: "Thomas Manz thomasamanz . gmail.com" To: CCL Subject: CCL: wiberg bond index Message-Id: <-51858-151104222224-8605-Tj4H7LK1zMY+9YjPO30VWA^server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a114aa086da47e40523c2a10a Date: Wed, 4 Nov 2015 20:22:09 -0700 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz:_:gmail.com] --001a114aa086da47e40523c2a10a Content-Type: text/plain; charset=UTF-8 For a hydrogen bond, you will likely see a bond order of ~0.1 between the hydrogen atom and the atom it is hydrogen-bonded to. The bond order and bond length can provide useful quantification of the hydrogen bond. On Mon, Nov 2, 2015 at 11:03 AM, Partha Sengupta anapspsmo]|[gmail.com < owner-chemistry_-_ccl.net> wrote: > Sir, How can I quantitatively infer the existence of intramolecular > hydrogen bond from the data obtained? > Partha > > On Mon, Nov 2, 2015 at 9:08 PM, Thomas Manz thomasamanz**gmail.com < > owner-chemistry-*-ccl.net> wrote: > >> Hi Partha, >> >> If you compute the Wiberg bond index in the NAO basis using the NBO >> program (NBO keyword BNDIDX), it gives a reasonable quantification of bond >> order in many cases >> (for hydrogen or other kinds of bonds, whether intermolecular or >> intramolecular). >> >> For spin polarized systems, you have to add twice the sum of the spin-up >> (alpha) and spin-down (beta) Wiberg bond indices to get the approximate >> bond order. >> For spin unpolarized systems, the Wiberg bond indices of the total >> electron density matrix is used, with no multiplication by two. >> >> Effective bond orders quantify the approximate number of electrons >> exchanged between two atoms. >> >> Tom >> >> On Sun, Nov 1, 2015 at 10:23 PM, Partha Sengupta anapspsmo%%gmail.com < >> owner-chemistry-x-ccl.net> wrote: >> >>> Friends, I have a question "how Wiberg bond index is related to >>> intramolecular hydrogen bond ?" >>> Partha >>> >>> -- >>> >>> >>> *Dr. Partha Sarathi SenguptaAssociate ProfessorVivekananda >>> Mahavidyalaya, Burdwan* >>> >> >> > > > -- > > > *Dr. Partha Sarathi SenguptaAssociate ProfessorVivekananda Mahavidyalaya, > Burdwan* > --001a114aa086da47e40523c2a10a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
For a hydrogen bond, you will likely see a bond order= of ~0.1 between the hydrogen atom and the atom it is hydrogen-bonded to. T= he bond order and bond length can provide useful quantification of the hydr= ogen bond.

On Mon, Nov 2, 2015 at 11:03 AM, Partha Sengupta anapspsmo]|[gmail.com <owner-chemistry_-_ccl.net> wrote:
Sir, How can= I quantitatively infer the existence =C2=A0of intramolecular hydrogen bond= from the data obtained?
Partha
<= br>
On Mon, Nov 2, 2015 at 9:08 PM, Thomas Manz t= homasamanz**gmail.com <owner-chemistry-*-ccl.net> wrote:
Hi Partha,

If you comput= e the Wiberg bond index in the NAO basis using the NBO program (NBO keyword= BNDIDX), it gives a reasonable quantification of bond order in many cases<= /div>
(for hydrogen or other kinds of bonds, whether intermolecular or = intramolecular).

For spin polarized systems, you h= ave to add twice the sum of the spin-up (alpha) and spin-down (beta) Wiberg= bond indices to get the approximate bond order.
For spin unpolar= ized systems, the Wiberg bond indices of the total electron density matrix = is used, with no multiplication by two.

Effective = bond orders quantify the approximate number of electrons exchanged between = two atoms.

Tom

On Sun, Nov 1, 2015 at 10:23 PM, Part= ha Sengupta anapspsmo%%gmail= .com <owner-chemistry-x-ccl.net> wrote:
Friends, I have a question = "how Wiberg bond index =C2=A0is related to intramolecular =C2=A0 hydro= gen bond ?"
Partha

--
= Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda= Mahavidyalaya, Burdwan




--
Dr. Partha Sarathi Sengupta
Associate Professor
Vivekanand= a Mahavidyalaya, Burdwan
--001a114aa086da47e40523c2a10a-- From owner-chemistry@ccl.net Wed Nov 4 23:05:01 2015 From: "Tian Lu sobereva*o*sina.com" To: CCL Subject: CCL: DOS calculations with G09 Message-Id: <-51859-151104230333-8033-TrpbKdocZqd4gHZhuiHQkQ()server.ccl.net> X-Original-From: "Tian Lu" Date: Wed, 4 Nov 2015 23:03:12 -0500 Sent to CCL by: "Tian Lu" [sobereva##sina.com] Hi, You only need to provide the .fch of the whole molecule at its final geometry to Multiwfn program, the .fch file of fragments are not required, so you don't need to consider the problem you mentioned. -------------------------------- Best wishes, Tian Lu Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China ----- Original Message ----- > From: "rayen mahi mahi.rayen===gmail.com" To: "Lu, Tian " Subject: CCL:G: DOS calculations with G09 Date: 2015-11-05 01:26 Thank you all for your help The system that I am working on is constituted by 2 fragments during the optimization of the structure I had to freeze the atoms that doesn't intervene in the interactions between the fragments. should I do the same thing during DOS calculation?