Mehboob

On Mon,= Apr 30, 2012 at 9:55 AM, Daniele Dondi kaliumster_+_gmail.com <owner-chemistry-$-ccl.net> wrote:<= br>

You need a parallel version of Gaussian to d= o that.

DD

2012/4/30 alireza zeina= li ar.zeinali,+,yahoo.com <owner-chemistry*ccl.net>

<= /table>

--bcaec554d63c0dfcdc04bee1751d-- From owner-chemistry@ccl.net Mon Apr 30 06:48:00 2012 From: "Serdar Bado?lu sbadoglu,gazi.edu.tr" To: CCL Subject: CCL:G: use of four processors in one computer for Gaussian program Message-Id: <-46815-120430064622-32298-/COChbspKCb8gIdBYLCb2Q_._server.ccl.net> X-Original-From: "Serdar Bado?lu" Content-Type: text/plain; charset="iso-8859-9" Date: Mon, 30 Apr 2012 10:35:35 -0000 Sent to CCL by: "Serdar Bado?lu" [sbadoglu#gazi.edu.tr] Dear Alireza, You should check your log file. Open it with note pad seek for the line saying "Will use up to X processors via shared memory." If X is 4 then no problem. If X is 1, this means that you are using the single seat / serial version of Gaussian. Regards. On Mon, Apr 30, 2012, "alireza zeinali ar.zeinali,+,yahoo.com" dedi: > Dear ccl-netters, > > > I have a quad-core computer on which I have submitted Gaussian program under windows. > > I tried to use the four processors in the computer by putting %nproc=4. However, when I > checked the task manager, I see only one processor is running. > > Anyone has idea how to make use of the four processors? > > Thank you > Alireza -- Serdar BADOGLU Gazi University Department of Physics From owner-chemistry@ccl.net Mon Apr 30 11:50:00 2012 From: "J.R. Schmidt schmidt*o*chem.wisc.edu" To: CCL Subject: CCL: Midwest Theoretical Chemistry Conference: Deadline FRIDAY, MAY 4 Message-Id: <-46816-120430110639-29215-MTxAZt+X4LwM6c4pQFPJpA(~)server.ccl.net> X-Original-From: "J.R. Schmidt" Date: Mon, 30 Apr 2012 11:06:38 -0400 Sent to CCL by: "J.R. Schmidt" [schmidt/./chem.wisc.edu] We are pleased to announce the 44th annual Midwest Theoretical Chemistry Conference, to be held June 7-9, 2012 on the campus of the University of Wisconsin-Madison. For 44 years, the MWTCC has been a distinctive meeting where students, faculty, and scientists come together in a relaxed environment to share their latest results in theoretical and computational chemistry. The abstract submission window and early registration period closes on THIS FRIDAY May 4, so register soon! We would also encourage all conference attendees to consider attending the associated Q-Chem workshop, to be held immediately prior to the start of MWTCC. MWTCC will be held June 7-9, 2012 on the campus of the University of Wisconsin-Madison. The conference will begin in the early evening of Thursday, June 7, and around noon on Saturday, June 9. Registration information and abstract submission are now available online at: http://www.mwtcc.org The conference registration fee is $70 for students, postdocs and faculty. The abstract submission window and early registration period closes on May 4, so please make sure to register soon! An additional $30 fee will be assessed for all registrations after this date. This fee includes all meals during the conference period (excluding dinner on Thursday, June 7th). Note the attendees must register separately for both the conference and for housing! We would also like to bring your attention to another opportunity in conjunction with MWTCC. One of the conference sponsors, Q-Chem Inc., will hold a workshop immediately prior to the start of MWTCC, the afternoon of June 7th. Q-Chem is a comprehensive ab initio package and the recent release of Q-Chem 4.0 includes many of the latest developments in quantum methodology. Please check their website for details: http://www.q-chem.com/qchem-website/wsmtcc_hh.html We hope to see you at the MWTCC in June! Sincerely, J.R. Schmidt Qiang Cui MWTCC co-organizers Department of Chemistry University of Wisconsin - Madison From owner-chemistry@ccl.net Mon Apr 30 14:08:01 2012 From: "George Fitzgerald George.Fitzgerald]=[accelrys.com" To: CCL Subject: CCL: response function Message-Id: <-46817-120430140226-30586-kOzC4J0BcAaMiIYkXvMrLA : server.ccl.net> X-Original-From: George Fitzgerald Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_55AC410F3302E740AC9EC50011F73E8F041AB92CBEEXCH1COLOacce_" Date: Mon, 30 Apr 2012 11:01:34 -0700 MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [George.Fitzgerald]^[accelrys.com] --_000_55AC410F3302E740AC9EC50011F73E8F041AB92CBEEXCH1COLOacce_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I thought that 'response function' referred simply to the electronic respon= se to some perturbation. For example, the perturbation could be geometric, = which gives you vibrational frequencies. Or magnetic, which gives you NMR s= hifts. The Fukui function is the response of the charge density to a change= in the occupation of the frontier orbitals. Is that the sort of informati= on you're looking for? George Fitzgerald, Ph.D. George.Fitzgerald__accelrys.com Advisory Scientist Accelrys, Inc. 10188 Telesis Ct San Diego CA 92121 +1 858 799 5360 (office) +1 858 692 8722 (mobile) > From: owner-chemistry+gfitzgerald=3D=3Daccelrys.com__ccl.net [mailto:owner-c= hemistry+gfitzgerald=3D=3Daccelrys.com__ccl.net] On Behalf Of partha sengupt= a anapspsmo*gmail.com Sent: Sunday, April 29, 2012 12:11 PM To: George Fitzgerald Subject: CCL: response function Friends, How response function relates the chemical reactivity indexes foor= a reactio? Is there any relation between Fukui function and Response funct= ion Partha sarathi Sengupta -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --_000_55AC410F3302E740AC9EC50011F73E8F041AB92CBEEXCH1COLOacce_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
I thought= that ‘response function’ referred simply to the electronic res= ponse to some perturbation. For example, the perturbation could be geometri= c, which gives you vibrational frequencies. Or magnetic, which gives you NM= R shifts. The Fukui function is the response of the charge density to a cha= nge in the occupation of the frontier orbitals. Is that the sort of i= nformation you’re looking for?

&nb= sp;

George Fitzgerald, Ph.D.
=
George.Fitzgerald__accelrys.com
Advisory Scientist
Accelrys, Inc.
10188 Telesis Ct
<= span style=3D'font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F= 497D'>San Diego CA 92121
+= 1 858 799 5360 (office)
+1= 858 692 8722 (mobile)

From:= owner-c= hemistry+gfitzgerald=3D=3Daccelrys.com__ccl.net [mailto:owner-chemistry+gfit= zgerald=3D=3Daccelrys.com__ccl.net] On Behalf Of partha sengupta anap= spsmo*gmail.com
Sent: Sunday, April 29, 2012 12:11 PM
To: George Fitzgerald
Subject: CCL: response function

Fri= ends, How response function relates the chemical reactivity indexes foor a = reactio? Is there any relation between Fukui function and Response function=
Partha sarathi Sengupta

--
Dr. Partha Sarathi Se= ngupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan
= --_000_55AC410F3302E740AC9EC50011F73E8F041AB92CBEEXCH1COLOacce_-- From owner-chemistry@ccl.net Mon Apr 30 15:00:00 2012 From: "David A Mannock dmannock|-|ualberta.ca" To: CCL Subject: CCL:G: use of four processors in one computer for Gaussian program Message-Id: <-46818-120430145620-28888-D01zSfnM0pHk4dq0iERBgw||server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=f46d04016807084f0104beea02d6 Date: Mon, 30 Apr 2012 12:56:12 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock:+:ualberta.ca] --f46d04016807084f0104beea02d6 Content-Type: text/plain; charset=ISO-8859-1 If you are using the MS Windows version of Gaussian the number of processors used may be 1. I think that the Win parallel versions of 03 and 09 are expensive. If you have a linux version, there are still bottle necks in some parts of the code that only use 1 core. In that case open a terminal and type top and you will see a list of processes. Check with the Gaussian manual online. David On Mon, Apr 30, 2012 at 4:35 AM, Serdar Bado?lu sbadoglu,gazi.edu.tr < owner-chemistry|*|ccl.net> wrote: > > Sent to CCL by: "Serdar Bado?lu" [sbadoglu#gazi.edu.tr] > Dear Alireza, > > You should check your log file. Open it with note pad seek for the line > saying "Will use up to X processors via shared memory." If X is 4 then > no problem. If X is 1, this means that you are using the single seat / > serial version of Gaussian. > > Regards. > > > On Mon, Apr 30, 2012, "alireza zeinali ar.zeinali,+,yahoo.com" > dedi: > > > Dear ccl-netters, > > > > > > I have a quad-core computer on which I have submitted Gaussian program > under windows. > > > > I tried to use the four processors in the computer by putting %nproc=4. > However, when I > > checked the task manager, I see only one processor is running. > > > > Anyone has idea how to make use of the four processors? > > > > Thank you > > Alireza > > -- > Serdar BADOGLU > Gazi University > Department of Physics> > > --f46d04016807084f0104beea02d6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable If you are using the MS Windows version of Gaussian the number of processor= s used may be 1. I think that the Win parallel versions of 03 and 09 are ex= pensive. If you have a linux version, there are still bottle necks in some = parts of the code that only use 1 core. In that case open a terminal and ty= pe top and you will see a list of processes. Check with the Gaussian manual= online. David

On Mon, Apr 30, 2012 at 4:35 AM, Serdar Bado= ?lu sbadoglu,gazi.edu.tr <owner-c= hemistry|*|ccl.net> wrote:

Sent to CCL by: "Serdar Bado?lu" [sbadoglu#gazi.edu.tr]
Dear Alireza,

You should check your log file. Open it with note pad seek for the line
saying "Will use up to =A0 =A0X processors via shared memory." If= X is 4 then
no problem. If X is 1, this means that you are using the single seat /
serial version of Gaussian.

Regards.

On Mon, Apr 30, 2012, "alireza zeinali ar.zeinali,+,yahoo.com"
<owner-chemistry-*-ccl.net<= /a>> dedi:

> Dear ccl-netters,
>
>
> I have a quad-core computer on which I have submitted Gaussian program= under windows.
>
> I tried to use the four processors in the computer by putting %nproc= =3D4. However, when I
> checked the task manager, I see only one processor is running.
>
> Anyone has idea how to make use of the four processors?
>
> Thank you
> Alireza

--
Serdar BADOGLU
Gazi University
Department of Physics

-=3D This is automatically added to each message by the mailing script =3D-=
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--f46d04016807084f0104beea02d6-- From owner-chemistry@ccl.net Mon Apr 30 18:06:00 2012 From: "Victor M Rosas-Garcia rosas.victor|gmail.com" To: CCL Subject: CCL: prediction of fluorescence? Message-Id: <-46819-120430174358-17132-XnKohn8YlVvx9BI8GNcv6g{=}server.ccl.net> X-Original-From: "Victor M Rosas-Garcia" Date: Mon, 30 Apr 2012 17:43:56 -0400 Sent to CCL by: "Victor M Rosas-Garcia" [rosas.victor/./gmail.com] Hello everybody, I was recently approached by a colleague, asking me if I could predict fluorescent behavior of a molecule. I understand that TD-DFT can be used for calculating excited states and things like UV-vis spectra, after a cursory review of the literature I have found some papers dealing with calculation of excited states of fluorescent molecules, but as far as predicting if a molecule will *actually* fluoresce, I don't know how to calculate this, or even if it is possible. The species of interest are around 300 amu, so probably I will not be able to do some super-duper cc-pV5Z calculations or the like. Any pointers? Victor From owner-chemistry@ccl.net Mon Apr 30 18:54:01 2012 From: "Keith Refson Keith.Refson[a]stfc.ac.uk" To: CCL Subject: CCL: Raman Phonon Calculations Message-Id: <-46820-120430161526-26568-tjsqHzyWAGpyuzcLcfEkSw^-^server.ccl.net> X-Original-From: Keith Refson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Mon, 30 Apr 2012 21:15:21 +0100 MIME-Version: 1.0 Sent to CCL by: Keith Refson [Keith.Refson^-^stfc.ac.uk] Dear Matthew, You write that you need to calculate Raman intensities as well as frequencies. While many solid state codes are able to compute frequencies (possibly with the aid of an external lattice dynamics driver program) there are few which can calculate activity. The only ones known to me are CASTEP (Disclosure: I and Phil Hasnip are developers of CASTEP), Quantum Espresso (mentioned by Rafal Korlacki) and also ABINIT. According to its website, VASP does not have the capability to compute Raman activities. With 60 atoms in the unit cell, benzoic acid should be within range for a medium to large compute cluster, and smaller than some I have done using CASTEP. Quantum Espresso does use a more efficient method, although we are working on a faster implementation. Keith Refson On 27/04/12 02:15, Matthew Reish mreish---chemistry.otago.ac.nz wrote: > Sent to CCL by: "Matthew Reish" [mreish#,#chemistry.otago.ac.nz] > General question but any help would be appreciated. I find myself needing to > calculate Raman active phonon energies and intensities of crystalline benzoic > acid and not sure how to get started. A google search makes it seem that using > the VASP program to calculate force constants then export this into a separate > program to calculate phonon modes is a common method used but seems fairly > complex. Before I begin using the VASP method I want to make sure this is the > best way for me to proceed. Any advice for a novice to calculating phonons > would be helpful. > > Cheers, > Matthew Reish > > Chemistry Department > University of Otago > Dunedin, New Zealand -- Dr Keith Refson, Building R25A STFC Rutherford Appleton Laboratory Harwell Science and Innovation Campus Chilton Didcot Oxfordshire OX11 0QX T: 01235 778023 Keith.Refson(_)(_)stfc.ac.uk -- Scanned by iCritical. From owner-chemistry@ccl.net Mon Apr 30 19:45:00 2012 From: "James T Metz James.Metz^^Abbott.com" To: CCL Subject: CCL: Prediction of fluorescence Message-Id: <-46821-120430194251-16367-mFLE6bYglsg28FWtt7RFxg*o*server.ccl.net> X-Original-From: "James T Metz" Date: Mon, 30 Apr 2012 19:42:44 -0400 Sent to CCL by: "James T Metz" [James.Metz**Abbott.com] Victor, Regarding the prediction of fluorescence, I asked this question from a slightly different angle in approx. August 2011 (can't find my original message). I was specifically interested in the availability of small molecule data sets with measured fluorescence to be used to create pattern recognition type models e.g., number of conjugated double bonds, attached EDGs or EWGs, number of aromatic rings, etc., rather than trying to use semi-empirical, ab initio, DFT, or some other (more) computationally intense method. I think it is clear that prediction of fluorescence might be helpful as a flag or warning with respect to results from HTS assays and might help avoid assay artifacts. Hence, if you or someone knows of published, quality data in this regard, I am still very interested. Thank you. Regards, Jim Metz Abbott Laboratories From owner-chemistry@ccl.net Mon Apr 30 20:19:00 2012 From: "Jim Kress ccl_nospam%%kressworks.com" To: CCL Subject: CCL: prediction of fluorescence? Message-Id: <-46822-120430201741-764-3hQ1sqbLGWEkS64JajNzDQ-$-server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Apr 2012 20:17:30 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam|*|kressworks.com] ORCA provides excellent tools that will allow calculation of UV/ Vis spectra, including fluorescence. Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com .. ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com .. ccl.net] On Behalf > Of Victor M Rosas-Garcia rosas.victor|gmail.com > Sent: Monday, April 30, 2012 5:44 PM > To: Kress, Jim > Subject: CCL: prediction of fluorescence? > > > Sent to CCL by: "Victor M Rosas-Garcia" [rosas.victor/./gmail.com] Hello > everybody, > > I was recently approached by a colleague, asking me if I could predict > fluorescent behavior of a molecule. I understand that TD-DFT can be used for > calculating excited states and things like UV-vis spectra, after a cursory > review of the literature I have found some papers dealing with calculation of > excited states of fluorescent molecules, but as far as predicting if a molecule > will *actually* fluoresce, I don't know how to calculate this, or even if it is > possible. > The species of interest are around 300 amu, so probably I will not be able to > do some super-duper cc-pV5Z calculations or the like. > > Any pointers? > > VictorTo > 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 look up the X- > Original-From: line in the mail header.> From owner-chemistry@ccl.net Mon Apr 30 23:01:00 2012 From: "Prof. Dr. N. Sekar nethi.sekar[a]gmail.com" To: CCL Subject: CCL: Prediction of fluorescence Message-Id: <-46823-120430225956-19964-jmeW+r7UxV3mQ+3l9g1ExQ*server.ccl.net> X-Original-From: "Prof. Dr. N. Sekar" Content-Type: multipart/alternative; boundary=14dae9340ef768c89304bef0c300 Date: Tue, 1 May 2012 08:29:46 +0530 MIME-Version: 1.0 Sent to CCL by: "Prof. Dr. N. Sekar" [nethi.sekar]*[gmail.com] --14dae9340ef768c89304bef0c300 Content-Type: text/plain; charset=ISO-8859-1 Dear Jim Metz, One could do TDDFT to odtain several excites states, optimize the low lying state, confirm that there are no many imaginary frequecies. and considering this as the emissive state one can see whether observed fluoesecence is same or different. I have not come across anything on the prediction of fluorescence. There are some papers discussing the quantum yield of fluorescent molecules. On Tue, May 1, 2012 at 5:12 AM, James T Metz James.Metz^^Abbott.com < owner-chemistry(-)ccl.net> wrote: > > Sent to CCL by: "James T Metz" [James.Metz**Abbott.com] > Victor, > > Regarding the prediction of fluorescence, I asked this question from a > slightly different angle in approx. August 2011 (can't find my original > message). I was specifically interested in the availability of small > molecule data sets with measured fluorescence to be used to create pattern > recognition type models e.g., number of conjugated double bonds, attached > EDGs or EWGs, number of aromatic rings, etc., rather than trying to use > semi-empirical, ab initio, DFT, or some other (more) computationally > intense method. > > I think it is clear that prediction of fluorescence might be helpful as a > flag or warning with respect to results from HTS assays and might help > avoid assay artifacts. > > Hence, if you or someone knows of published, quality data in this regard, > I am still very interested. > > Thank you. > > Regards, > Jim Metz > > Abbott Laboratories> > > -- Thanks and regards Prof. Dr. N. Sekar CCol FSDC Co-ordinator, UGC-CAS and Professor in Tinctorial Chemistry Dyestuff Technology Department Institute of Chemical Technology (formerly UDCT) Matunga, Mumbai-400019 Mob +91-9867958452 n.sekar(-)ictmumbai.edu.in sekarnm(-)rediffmail.com drnsekar4562000(-)yahoo.co.in website: http://ictmumbai.edu.in/Fac_FacDetails.aspx?fidno=116 --14dae9340ef768c89304bef0c300 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Jim Metz,
One could do TDDFT=A0to odtain=A0several exci= tes states, optimize the low lying state, confirm that there are no many im= aginary frequecies. and considering this as the emissive state one can see = whether observed fluoesecence is same or different.=A0 I have not come acro= ss anything on the prediction of fluorescence.=A0 There are some papers dis= cussing the quantum yield of fluorescent molecules.

On Tue, May 1, 2012 at 5:12 AM, James = T Metz James.Metz^^Abbott.com <owner-chemistry(-)ccl.net> wrote:

Sent to CCL by: "James T Metz" [James.Metz**Abbott.com]
Victor,

Regarding the prediction of fluorescence, I asked this question from a slig= htly different angle in approx. August 2011 (can't find my original mes= sage). =A0I was specifically interested in the availability of small molecu= le data sets with measured fluorescence to be used to create pattern recogn= ition type models e.g., number of conjugated double bonds, attached
EDGs or EWGs, number of aromatic rings, etc., rather than trying to use sem= i-empirical, ab initio, DFT, or some other (more) computationally intense m= ethod.

I think it is clear that prediction of fluorescence might be helpful as a f= lag or warning with respect to results from HTS assays and might help avoid= assay artifacts.

Hence, if you or someone knows of published, quality data in this regard, I= am still very interested.

Thank you.

Regards,
Jim Metz

Abbott Laboratories

-=3D This is automatically added to each message by the mailing script =3D-=
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--
Thanks and regards=

Prof. Dr. N. Sekar=A0=A0 CCol FSDC
Co-ordinator, UGC-CAS and Pro= fessor in Tinctorial Chemistry
Dyestuff Technology Department
Institu= te of Chemical Technology (formerly UDCT)
Matunga, Mumbai-400019

Mob +91-9867958452
n.sekar(-)ictmumbai.edu.in
sekarnm(-)rediffmail.= com
drnsekar45= 62000(-)yahoo.co.in

=A0

website: http://ictmumbai.edu.in/Fac_FacDetails.aspx?fidno= =3D116

--14dae9340ef768c89304bef0c300--
Dear ccl-n= etters,

I have a quad-core computer on which I have submitted Gaussian prog= ram under windows.

I tried to use the four processors in the compute= r by putting %nproc=3D4. However, when I
checked the task manager, I see= only one processor is running.

Anyone has idea how to make use of the four processors?

Thank yo= u
Alireza