From owner-chemistry@ccl.net Thu Jul 19 09:18:00 2012 From: "John Keith john.keith]-[gmail.com" To: CCL Subject: CCL: positive energy of the frontier orbital Message-Id: <-47237-120719091624-12746-WmQEvv2jlar82RvkNCpBvg~!~server.ccl.net> X-Original-From: John Keith Content-Type: multipart/alternative; boundary=f46d04451743be830404c52e9527 Date: Thu, 19 Jul 2012 09:16:18 -0400 MIME-Version: 1.0 Sent to CCL by: John Keith [john.keith__gmail.com] --f46d04451743be830404c52e9527 Content-Type: text/plain; charset=ISO-8859-1 Dear Prof. Jensen, do you have a preferred reference showing the importance of diffuse functions in the ~1E-04 range you suggested? Some CCL readers may want to be aware that those exponents are more than 10 to 100 times smaller than the smallest exponents for diffuse functions found in the EMSL basis set library. Best regards, --john On Wed, Jul 18, 2012 at 7:56 PM, Frank Jensen frj[]chem.au.dk < owner-chemistry:_:ccl.net> wrote: > > Sent to CCL by: Frank Jensen [frj#,#chem.au.dk] > A positiv HOMO energy means that the total energy can be lowered by > removing some of the electron density. A free electron has an 'orbital' > energy of zero, thus in a sufficiently flexible basis set, the electron > density in the HOMO can be transfered to a free electron state, and give a > lower energy state. > > This is common when using DFT for anions, where transfer of a fraction of > the HOMO density to an unbound electron 'orbital' gives a lower energy > state. > > Note that a 'sufficiently flexible basis set' is not just your favorite > basis set augmented with diffuse functions, it must contain diffuse > functions with exponents in ~10^-4 or less range. > > Frank > > > > > Citat af "may abdelghani may01dz[*]yahoo.fr" : > > >> >> Dear CCL'ers >> >> If the frontier orbital >> (HOMO's) energy of a compound have a positive value, is this a conclusive >> evidence >> that this compound is a unstable >> one. >> A.May >> >> >> > > > Frank Jensen > Assoc. Prof. > Dept. of Chemistry > Aarhus University > http://old.chem.au.dk/~frj> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message > Job: http://www.ccl.net/**jobsConferences: > http://server.ccl.net/**chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --f46d04451743be830404c52e9527 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Prof. Jensen, do you have a preferred reference showing the importance= of diffuse functions in the ~1E-04 range you suggested?=A0 Some CCL reader= s may want to be aware that those exponents are more than 10 to 100 times s= maller than the smallest exponents for diffuse functions found in the EMSL = basis set library. =A0

Best regards,

--john

On Wed, = Jul 18, 2012 at 7:56 PM, Frank Jensen frj[]ch= em.au.dk <owner-chemistry:_:ccl.net> wrote:

Sent to CCL by: Frank Jensen [frj#,#chem.au.dk]
A positiv HOMO energy means that the total energy can be lowered by removin= g some of the electron density. A free electron has an 'orbital' en= ergy of zero, thus in a sufficiently flexible basis set, the electron densi= ty in the HOMO can be transfered to a free electron state, and give a lower= energy state.

This is common when using DFT for anions, where transfer of a fraction of t= he HOMO density to an unbound electron 'orbital' gives a lower ener= gy state.

Note that a 'sufficiently flexible basis set' is not just your favo= rite basis set augmented with diffuse functions, it must contain diffuse fu= nctions with exponents in ~10^-4 or less range.

Frank




Citat af "may abdelghani may01dz[*]yahoo.fr" <owner-chemistry/a\ccl.net>:



Dear CCL'ers

If=A0 the frontier orbital
(HOMO's) energy of a compound have a positive value, is this a conclusi= ve evidence
that this compound is a unstable
one.
A.May





Frank Jensen
Assoc. Prof.
Dept. of Chemistry
Aarhus University
http://old.chem.= au.dk/~frj



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--f46d04451743be830404c52e9527-- From owner-chemistry@ccl.net Thu Jul 19 10:40:01 2012 From: "Christopher Hansen csh297 * uowmail.edu.au" To: CCL Subject: CCL:G: G09 CASSCF # of processors. Message-Id: <-47238-120719010627-10756-q2PtODUJTBc3kFqxRzvG2Q _ server.ccl.net> X-Original-From: "Christopher Hansen" Date: Thu, 19 Jul 2012 01:06:25 -0400 Sent to CCL by: "Christopher Hansen" [csh297:uowmail.edu.au] Dear CCLers, I've been doing a number of CASSCF optimisation and frequency calcs using Gaussian 09. I've been submitting them on 8 CPUs and have recently noticed that my CPU usage is only ever ~16%. This isn't the case for other types of calculation. This seems to suggest to me that I am not making full use of my processors. How does the performance of these CASSCF calculations in Gaussian scale with the number of processors? Does Gaussian even spread the load over the processors when these calcs are run in parallel? Thank you. Sincerely, Chris From owner-chemistry@ccl.net Thu Jul 19 11:15:00 2012 From: "Gabriele Cruciani gabri(a)chemiome.chm.unipg.it" To: CCL Subject: CCL: Latest issue of Foundations of Chemistry Message-Id: <-47239-120719041947-2286-b5YGQwyATRvUnqjGzXRnkQ(0)server.ccl.net> X-Original-From: Gabriele Cruciani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Jul 2012 10:19:50 +0200 MIME-Version: 1.0 Sent to CCL by: Gabriele Cruciani [gabri!^!chemiome.chm.unipg.it] Andreas, Ulf, I perfectly agree with you. We already have lot of noise in this list, we do not need more. G.Cruciani, University of Perugia > Dear Colleagues, > > I do agree with Mr. Ekstrom. > > Best wishes, > > Dr. András Péter Borosy > Scientific Modelling Expert > > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf - > Switzerland > T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com > > > >> From: "uekstrom ~~ gmail.com uekstrom ~~ gmail.com" > > To: "Borosy, Andras " > Date: 18.07.2012 09:45 > Subject: CCL: Latest issue of Foundations of Chemistry > Sent by: owner-chemistry+andras.borosy==givaudan.com[a]ccl.net > > > > > Sent to CCL by: "uekstrom]_[gmail.com" [uekstrom]_[gmail.com] > Dear Tom, > I did not mean that no subscriber to CCL is interested in Frontiers of > Chemistry. What I meant was that Eric Scerri could use one or two > sentences in his posts to write _why_ CCL subscribers should check out > his blog posts or journal issues. You may note that he has not replied > (on CCL at least) to any of the people discussing his blog posts. On > is tempted to think that he just posts them here to get more readers, > and is not really interested in discussion about computational > chemistry. > > Regards, > Ulf Ekstrom, University of Oslohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt--=_alternative 002ADE9BC1257A3F_Content-Type: text/html; charset="ISO-8859-1" > Content-Transfer-Encoding: quoted-printable > > Dear Colleagues, >
>
I do agree with Mr. Ekstrom. >
>
Best wishes, >
>
Dr. András Péter Borosy
> Scientific Modelling Expert
>
> Fragrance Research
> Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 >  - Dübendorf - Switzerland
> T:+41-44-824 2164 - F:+41-44-8242926  - http://www.givaudan.com >
>
>
>
From:    >  "uekstrom ~~ gmail.com > uekstrom ~~ gmail.com"<owner-chemistry[a]ccl.net> >
To:    >  "Borosy, Andras > "<andras.borosy[a]givaudan.com> >
Date:    >  18.07.2012 09:45 >
Subject:   >   CCL: Latest > issue of Foundations of Chemistry >
Sent by:   >   owner-chemistry+andras.borosy==givaudan.com[a]ccl.net >
>
>
>
>

> Sent to CCL by:"uekstrom]_[gmail.com" [uekstrom]_[gmail.com]
> Dear Tom,
> I did not mean that no subscriber to CCL is interested in Frontiers of
> Chemistry. What I meant was that Eric Scerri could use one or two
> sentences in his posts to write _why_ CCL subscribers should check out
> his blog posts or journal issues. You may note that he has not replied
> (on CCL at least) to any of the people discussing his blog posts. On
> is tempted to think that he just posts them here to get more readers,
> and is not really interested in discussion about computational
> chemistry.
>
> Regards,
> Ulf Ekstrom, University of Oslo
>
>
> > >    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
>
> Before posting, check wait time at:http://www.ccl.net
>
> Job:http://www.ccl.net/jobs >
> Conferences:http://server.ccl.net/chemistry/announcements/conferences/
>
> Search Messages:http://www.ccl.net/chemistry/searchccl/index.shtml
> >    http://www.ccl.net/spammers.txt
>
> RTFI:http://www.ccl.net/chemistry/aboutccl/instructions/
>
>
> >
From owner-chemistry@ccl.net Thu Jul 19 11:50:00 2012 From: "Maria Saeed mariyasaeed^^yahoo.com" To: CCL Subject: CCL: how to align the protein in popc membrane using NAMD Message-Id: <-47240-120719052346-10786-+4gZDyeX03a93fLVFd5IAQ#%#server.ccl.net> X-Original-From: Maria Saeed Content-Type: multipart/alternative; boundary="1635569886-649566311-1342689820=:23350" Date: Thu, 19 Jul 2012 02:23:40 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Maria Saeed [mariyasaeed-.-yahoo.com] --1635569886-649566311-1342689820=:23350 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi all, please=0Aguide me how to align the protein in popc membrane using NAMD if w= e=0Aknow that the residue like 8 to 31 , 56 to 72=A0 , 91 to=A0 121 etc how= we=0Acan embed these residue in membrane while other remain outside the=0A= membrane how we can fix these residue in the membrane. please guide me=0Aif= anyone know about it. i will appreciate. Regards,=20 Maria Saeed --1635569886-649566311-1342689820=:23350 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable


Hi all,

please=0Aguide me how = to align the protein in popc membrane using NAMD if we=0Aknow that the resi= due like 8 to 31 , 56 to 72  , 91 to  121 etc how we=0Acan embed = these residue in membrane while other remain outside the=0Amembrane how we = can fix these residue in the membrane. please guide me=0Aif anyone know abo= ut it.
i will appreciate.

Regards,

= Maria Saeed


<= br style=3D"color: rgb(0, 0, 191);"><= a rel=3D"nofollow" target=3D"_blank" href=3D"http://zaheer%20qasmi">
--1635569886-649566311-1342689820=:23350-- From owner-chemistry@ccl.net Thu Jul 19 12:25:00 2012 From: "Francisco Hernandez-Guzman Francisco.Hernandez:_:accelrys.com" To: CCL Subject: CCL: 3D molecular modelling software Message-Id: <-47241-120719103858-18039-brIY9QqGpauglyPcbP7rnA__server.ccl.net> X-Original-From: Francisco Hernandez-Guzman Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Jul 2012 07:38:45 -0700 MIME-Version: 1.0 Sent to CCL by: Francisco Hernandez-Guzman [Francisco.Hernandez||accelrys.com] Hi Gustavo, Our free Discovery Studio Visualizer supports hardware stereo on most vendor systems including NVIDIA. http://accelrys.com/products/discovery-studio/visualization-download.php The free version allows you to do the visual analysis of molecules and trajectories. It contains molecular builders and many other features. The paid version extends the free version to allow you to do conformational analysis, MD, docking, stability prediction, and a lot more. Cheers, Francisco Sr. Product Manager Accelrys Software, Inc. -----Original Message----- > From: owner-chemistry+francisco.hernandez==accelrys.com * ccl.net [mailto:owner-chemistry+francisco.hernandez==accelrys.com * ccl.net] On Behalf Of Gustavo L.C. Moura gustavo.moura]*[ufpe.br Sent: Wednesday, July 18, 2012 2:01 PM To: Francisco Hernandez-Guzman Subject: CCL: 3D molecular modelling software Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura.:.ufpe.br] Dear CCL Readers, Would any of you know a molecular modelling software in 3D which can be used to visualize molecules, conformational analysis, molecular dynamics trajectories, docking, etc, using stereo glasses compatible with either NVIDIA 3D Vision or Blu-Ray? Thank you very much in advance. Sincerely yours, Gustavo L.C. Mourahttp://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 Thu Jul 19 13:41:00 2012 From: "Elaine Meng meng_._cgl.ucsf.edu" To: CCL Subject: CCL: 3D molecular modelling software Message-Id: <-47242-120719132019-20465-8mP5W3uUFnTp8/ljjoOc3g]_[server.ccl.net> X-Original-From: "Elaine Meng" Date: Thu, 19 Jul 2012 13:20:17 -0400 Sent to CCL by: "Elaine Meng" [meng===cgl.ucsf.edu] Hi Gustavo, Chimera includes tools for viewing trajectories and viewing docked compounds (several formats read), general molecular analysis, and a variety of stereo options. Chimera website: http://www.cgl.ucsf.edu/chimera/index.html The types of stereo you mention will work with Chimera ("sequential stereo") if the capability is exposed to OpenGL on your computer. In general this will require a workstation graphics card, except for some Macs. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Thu Jul 19 14:35:01 2012 From: "Venable, Richard (NIH/NHLBI) E venabler(-)nhlbi.nih.gov" To: CCL Subject: CCL: how to align the protein in popc membrane using NAMD Message-Id: <-47243-120719130708-13808-jsbe+4iVfhSRyLv9GQKmvw{:}server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Jul 2012 13:06:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler*nhlbi.nih.gov] I suggest a visit to www.charmm-gui.org which features a membrane system builder, and exports files for both CHARMM and NAMD packages. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov > From: "Barry Hardy barry.hardy*o*vtxmail.ch" > Reply-To: CCL Subscribers > Date: Thu, 19 Jul 2012 05:23:40 -0400 To: "Venable, Richard (NIH/NHLBI) [E]" > Subject: CCL: how to align the protein in popc membrane using NAMD Hi all, please guide me how to align the protein in popc membrane using NAMD if we know that the residue like 8 to 31 , 56 to 72 , 91 to 121 etc how we can embed these residue in membrane while other remain outside the membrane how we can fix these residue in the membrane. please guide me if anyone know about it. i will appreciate. Regards, Maria Saeed From owner-chemistry@ccl.net Thu Jul 19 20:58:00 2012 From: "Alan Shusterman alan-$-reed.edu" To: CCL Subject: CCL: iSpartan for iPad Message-Id: <-47244-120719204208-15005-aJMpIV1U0dICJSAwFHE48Q~~server.ccl.net> X-Original-From: Alan Shusterman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Jul 2012 17:42:28 -0700 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan]-[reed.edu] Chemists who would like a more convenient way to take their models 'on the road' now have a new modeling option for the iPad: iSpartan (Wavefunction, Inc.) One feature that is "entirely different" in this app is the input. Instead of clicking molecular fragments together, one sketches a structural formula (some bigger fragments can be "clicked" in). Your non-computational colleagues who could never figure out (or remember the workings of) a model input interface now can rely on something they already know how to do: draw. (They can also use the iPad as an input device for creating models for Spartan.) To find out more: > from Wavefunction - http://wavefun.com/products/iSpartan/ispartan_main.html a review from Macs in Chemistry blog - http://www.macinchem.org/blog/files/892bf4332a54f95e03cb3c5629eeecf6-1018.php > from iTunes app store - http://itunes.apple.com/us/app/ispartan/id534726646?mt=8 -Alan -- Alan Shusterman Chemistry Department Reed College Portland, OR 97202-8199 503-517-7699 http://blogs.reed.edu/alan/ "Nature doesn't make long speeches." Lao Tzu 23 From owner-chemistry@ccl.net Thu Jul 19 21:32:00 2012 From: "Frank Jensen frj!=!chem.au.dk" To: CCL Subject: CCL: positive energy of the frontier orbital Message-Id: <-47245-120719212410-25989-P4RThcxMw2gmP3S6rwjwkA_+_server.ccl.net> X-Original-From: Frank Jensen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 20 Jul 2012 03:23:56 +0200 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj.:.chem.au.dk] John, Indeed I do ;-) JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 6 Issue: 9 Pages: 2726-2735 Depending on your favorite program, you most likely need to make a few changes in the code and employ a few tricks to get the wave function to converge when using _very_ diffuse basis functions. Frank Citat af "John Keith john.keith]-[gmail.com" : > Dear Prof. Jensen, do you have a preferred reference showing the importance > of diffuse functions in the ~1E-04 range you suggested? Some CCL readers > may want to be aware that those exponents are more than 10 to 100 times > smaller than the smallest exponents for diffuse functions found in the EMSL > basis set library. > > Best regards, > > --john > > On Wed, Jul 18, 2012 at 7:56 PM, Frank Jensen frj[]chem.au.dk < > owner-chemistry++ccl.net> wrote: > >> >> Sent to CCL by: Frank Jensen [frj#,#chem.au.dk] >> A positiv HOMO energy means that the total energy can be lowered by >> removing some of the electron density. A free electron has an 'orbital' >> energy of zero, thus in a sufficiently flexible basis set, the electron >> density in the HOMO can be transfered to a free electron state, and give a >> lower energy state. >> >> This is common when using DFT for anions, where transfer of a fraction of >> the HOMO density to an unbound electron 'orbital' gives a lower energy >> state. >> >> Note that a 'sufficiently flexible basis set' is not just your favorite >> basis set augmented with diffuse functions, it must contain diffuse >> functions with exponents in ~10^-4 or less range. >> >> Frank >> >> >> >> >> Citat af "may abdelghani may01dz[*]yahoo.fr" : >> >> >>> >>> Dear CCL'ers >>> >>> If the frontier orbital >>> (HOMO's) energy of a compound have a positive value, is this a conclusive >>> evidence >>> that this compound is a unstable >>> one. >>> A.May >>> >>> >>> >> >> >> Frank Jensen >> Assoc. Prof. >> Dept. of Chemistry >> Aarhus University >> http://old.chem.au.dk/~frj> >> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message >> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message >> Job: >> http://www.ccl.net/**jobsConferences: >> http://server.ccl.net/**chemistry/announcements/**conferences/ >> >> Search Messages: >> http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt >> >> >> RTFI: >> http://www.ccl.net/chemistry/**aboutccl/instructions/ >> >> >> > Frank Jensen Assoc. Prof. Dept. of Chemistry Aarhus University http://old.chem.au.dk/~frj From owner-chemistry@ccl.net Thu Jul 19 23:31:01 2012 From: "Godwin Amo-Kwao amokwao/a\unm.edu" To: CCL Subject: CCL: Gaussian CI calculation output. Message-Id: <-47246-120719232927-14557-KrzdJU3GReRwxBsr9crwGw^server.ccl.net> X-Original-From: "Godwin Amo-Kwao" Date: Thu, 19 Jul 2012 23:29:24 -0400 Sent to CCL by: "Godwin Amo-Kwao" [amokwao###unm.edu] Hi, I am trying to get excited states energies for single atoms. I would like to compare the transition energies to the NIST database. I use this as my route section. ************************************************************************* #P opt cis=(singlets,nstates=1)/6-311++g(d,p) density=current pop=full ************************************************************************* I am getting the output in this form ********************************************************************* Excitation energies and oscillator strengths: Excited state symmetry could not be determined. Excited State 1: ?Spin -?Sym 0.1837 eV 6747.61 nm f=0.0000 3A -> 5A 0.87790 3A -> 9A -0.43212 3A -> 12A -0.15673 4A -> 5A 0.11337 This state for optimization and/or second-order correction. Total Energy, E(CIS) = -37.6828173939 *********************************************************************** Could you explain to me what the excited state transition 3A->5A etc mean? I have checked google and Foresman but still cannot decode this. Any pointers will be appreciated. Thank you.