From owner-chemistry@ccl.net Sun Oct 23 11:30:00 2011 From: "akhilesh sharma sh.akhilesh__gmail.com" To: CCL Subject: CCL:G: can GAUSS VIEW 4.1 Version use for visvalization of g09 outout files Message-Id: <-45717-111023025736-8622-+RisPBQKKCFoEoonnB5ekA],[server.ccl.net> X-Original-From: akhilesh sharma Content-Type: multipart/alternative; boundary=f46d0444014680253a04aff1d121 Date: Sun, 23 Oct 2011 12:27:23 +0530 MIME-Version: 1.0 Sent to CCL by: akhilesh sharma [sh.akhilesh]|[gmail.com] --f46d0444014680253a04aff1d121 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi another way to do this has also been described earlier in CCL *Change the lines =93Atom AN=94 with =93Atom AN=94. They look the same bu= t there are *TWO *spaces in the first (this is the way G09 prints the output files) and in the second one there is only *ONE *space. see http://server.ccl.net/chemistry/resources/messages/2009/10/08.007-dir/index= .html On 12 October 2011 17:36, Close, David M. CLOSED]*[mail.etsu.edu < owner-chemistry---ccl.net> wrote: > This was discussed some time ago on the CCL. I seem to recall that the > fault had to do with differences G03 and G09 write output files. It seem= s > that the solution was top first run formchk. **** > > ** ** > > *From:* owner-chemistry+closed=3D=3Detsu.edu---ccl.net [mailto: > owner-chemistry+closed=3D=3Detsu.edu---ccl.net] *On Behalf Of *sumit () > iiser,pune sumitkumar() iiserpune.ac.in > *Sent:* Wednesday, October 12, 2011 6:56 AM > *To:* Close, David M. > *Subject:* CCL:G: can GAUSS VIEW 4.1 Version use for visvalization of g09 > outout files**** > > ** ** > > Dear Friends,**** > > **** > > I am getting one very different kind of problem.**** > > when i am using *gauss view 4.1* to open the output file of *G03,* it was > opening but the same *gauss view 4.1* is not able to open *G09 *output > files.**** > > Please help me to came out from this problem > **** > > * > -------------------------------------------------------------------------= ------------------ > ***** > > *Sumit Kumar** > Research Scholar***** > > *(laser spectroscopy)** > Indian Institutes of Science Education and Research,pune***** > > * > -------------------------------------------------------------------------= ------------------- > ** > * > **** > > ** ** > > ** ** > --f46d0444014680253a04aff1d121 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Hi
another way to do this has also been described earlier in= CCL
*Change the lines =93Atom =A0 AN=94 with =93Atom AN=94. They= look the same but there are TWO spaces in the first (this= is the way G09 prints the output files) and in the second one there is onl= y ONE space.
=A0
see http://server.ccl.net/chemistry/re= sources/messages/2009/10/08.007-dir/index.html

On 12 October 2011 17:36, Close, David M. CLOSED]*[mail.etsu.edu <owner-chemistry---ccl.net> wrote:

This was disc= ussed some time ago on the CCL.=A0 I seem to recall that the fault had to d= o with differences G03 and G09 write output files.=A0 It seems that the sol= ution was top first run formchk.=A0

=A0

From:= owner-chemistry+closed=3D=3Detsu.edu---ccl.net [mailto:owner-chemistry+cl= osed=3D=3Detsu.ed= u---ccl.net] On Behalf Of sumit () iiser,pune sumitkumar() iiserpune.ac.in
Sent: Wednesday, October 12, 2011 6:56 AM
To: Close, David= M.
Subject: CCL:G: can GAUSS VIEW 4.1 Version use for visvalizat= ion of g09 outout files

=A0

Dear Friends,

=A0

I am getting one very different kind of problem.<= u>

when i am using gauss view 4.1 to open the output file of G03, it was opening but = the same gauss view 4.1 is not able to open G09 output files.

Please hel= p me to came out from this problem

=

-------------= ---------------------------------------------------------------------------= ---

Sumit K= umar
Research = Scholar

(laser spectroscopy)
Indian Institutes of Science Education and Research,pune

-------------------------------------------------------------= -------------------------------
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0

=A0

=A0


--f46d0444014680253a04aff1d121-- From owner-chemistry@ccl.net Sun Oct 23 17:18:00 2011 From: "K.Radacki K.Radacki-*-mail.uni-wuerzburg.de" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45718-111023062230-17257-YwSyLB6OeBDL6x7zq6wVEg_-_server.ccl.net> X-Original-From: "K.Radacki" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 23 Oct 2011 12:22:09 +0200 MIME-Version: 1.0 Sent to CCL by: "K.Radacki" [K.Radacki*o*mail.uni-wuerzburg.de] On 10/20/2011 11:25 AM, Georg Lefkidis lefkidis * physik.uni-kl.de wrote: > Sent to CCL by: "Georg Lefkidis" [lefkidis=physik.uni-kl.de] > Hello everyone, > > I don't know if this was brought to the list's attention already, but there > is an additional component as well (much as most of us would not like to > admit it). Writing a source code often is the most time consuming part of > one's results, even if the mathematical analysis per se might be done > relatively quickly. This means, that once a code is there, the author(s) > would like to use it over and over again (perhaps for different but similar > systems) and of course *publish* more. The algorithmic implementation of a > mathematical formula is part of the process. So I believe that most > scientists-programmers would not feel very comfortable with sharing the > codes with *anonymous* referees, which at the end might even reject the > paper, and see that work appear elsewhere for other systems. Let's not > forget it is not only the systems, the analysis and the results, but also > the programming itself that is worth a publication. Everyone who ever > programmed a data-mining algorithm for Gaussian or Gamess output knows that > only too well. > > Perhaps this is not of concern to great professors with huge groups and > meanwhile bug-free codes that have been around for decades but to a common > mortal (like myself) it is (since I've seen that happen, although luckily > not to me yet). Finally somebody touch this point. > Another issue is the quality of different third-party programs used. I read > a couple of posts below, that it is (or might be) that the group's > reputation is decisive. In fact there is more to that: being able to > evaluate the quality of the results (by comparing to experiment or assessing > the quality of derived properties, selection rules, symmetries etc.) plays > also a very big role. For me a paper interpreting the importance of scaling > a parameter done with not the best code is at least equally important as the > best uncommented results produces out of the code only. So I see a potential > danger there if the code itself becomes more and more important. Besides, > good results will always get reproduced by other groups even with other > codes or methods (for instance theory vs. experiment etc.). Actually I believe that the interpreting is more important that calculations. I've seen enough papers that claim to "shed a light into HERE TOPIC" but except saying what that did and how (what software, methods and so on) there is no explanation "why". On the end we want to understand chemistry, don't we? > I am not saying I am for or against those two arguments, I just want to > mention them as possible issues which need thinking. > > Best regards > Georg When ~15 years ago I started to use linux, I thought windows is bad, linux is good. Typical neophyte view point. I took me some years to see this one not in categories of black&white but some shades of grey. IMHO I think that part of the arguments for "availability of source" is black&white view point. I see advantages of manifesto but there is a realy world out there. Think about 1st part of Georg's mail. For me it's the time to be back in real world and start to work a bit ;-) Kris > -----Ursprüngliche Nachricht----- > Von: owner-chemistry+lefkidis==physik.uni-kl.de|-|ccl.net > [mailto:owner-chemistry+lefkidis==physik.uni-kl.de|-|ccl.net] Im Auftrag von > Andrew Dalke dalke a dalkescientific.com > Gesendet: Mittwoch, 19. Oktober 2011 11:39 > An: Lefkidis, Georg > Betreff: CCL: Science code manifesto > > > Sent to CCL by: Andrew Dalke [dalke^^^dalkescientific.com] On Oct 18, 2011, > at 4:17 PM, Adrià Cereto Massagué adrian.cereto,+,gmail.com wrote: >> I don't think the manifesto is at odds with FSF. GPL'd software can be > sold at any price, but its source code must be available for those who own > the software at no further cost. And someone who has bought some GPL > software is allowed to redistribute it for free, so researchers using it for > a paper would be able to provide the software to reviewers and readers of > the paper at no cost. > > Abstract: How much can the paper authors ask for access to the source code? > How much can the curators charge? What should the curator do if the curated > software contains a license violation? > > > If I write a paper which depends on software for its analysis, and others > should have access to the software as part of effective peer review, then > how much can I charge others to get access to the software? US $1 billion? > > The FSF says I can charge as much as you want, and that freedom is one of > the core freedoms of free software. > > The philosophy that others need access to my source code to provide good > peer review has the implicit assumption that I will provide the software at > a non-prohibitive cost. > > There is clearly a tension between these two viewpoints. This manifesto says > nothing of what that cost might be, nor even that it might be an issue. > > > What should be the cost to get access to source code from the author, or >> from the curator? Does the curator get no-cost access to it as a condition > of publication? Doesn't any limit on cost curtail what the FSF says is my > freedom to charge as much as I want? > > Remember, the FSF encourages software freedom. I argue that scientific > communication has overlapping but different goals. > Science communications needs to have a low cost so that many people can get > access to it. The FSF is only concerned about what happens *after* someone > gets access to software. > > > This is of course similar to (most) scientific papers. There the author > gives the curator the right to redistribute the paper without paying > royalties, and the curator can charge effectively any price for it. Most > paper publishers want to maximize revenue, and therefore set high but not > prohibitive prices. The software author may have other concerns. > > > Interestingly, the software curator takes on a more difficult challenge than > a paper curator. The authors of a paper (with a few exceptions usually > well-covered by fair use exceptions) are the only copyright holders of a > paper. More often though, the accompanying software has many more copyright > holders. That can lead to problems. > > Consider the CDK chemistry toolkit. The package contains many copyright > holders, including those from third-party libraries which it incorporates. A > few years ago the CDK was in minor violation of the LGPL requirement of some > of those libraries. > (It omitted the credit required by those licenses.) This was quickly fixed > once pointed out. I can easily imagine cases where it can't be easily fixed. > > The curator takes on the risk that someone else, who is a copyright holder > to the software in question but not a paper author, may challenge the right > of the curator to distribute the software. How does the curator resolve the > violation, especially if the original author doesn't want to be involved? > Does the curator remove the software in question? > > If so, and if you insist that the software must be available in order to do > correct peer review, then should the corresponding paper also be withdrawn? > > As I said before, these are solvable. I bring them up because I encourage > people to distribute their source code along with the paper, and to be aware > that it's not a simple, clear issue. > > > Andrew > dalke:+:dalkescientific.comhttp://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 Sun Oct 23 17:52:00 2011 From: "Sergio Emanuel Galembeck segalemb__usp.br" To: CCL Subject: CCL:G: AIM for molecular ion Message-Id: <-45719-111023172921-19485-nUbWYbG+otBbgDgCvY8d+A ~~ server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sun, 23 Oct 2011 19:29:07 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb{=}usp.br] Dear Dario, The use of AIM modules in Gaussian is not recommend, in part because this option is not maintained. I recommend the use of AIMAll, because this is a fast and robust program. Hope this help, Sergio Citando "Dario Fernando Coral ferchocoralg16 .. gmail.com" : > > Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16__gmail.com] > regards > > Does anyone know how to perform AIM calculations in gaussian 09 or > 03 for a molecular ion? > > I have performed this calculation for the neutral water molecule, > but when I use AIM command on the furfuryl-aniline molecular ion, > gaussian 09 has an error in the link L609 > > The route card I used is as follows: # ub3lyp/631g(d) AIM=charge test > > thanks in advance> > > From owner-chemistry@ccl.net Sun Oct 23 19:34:00 2011 From: "Johannes Hachmann jh[*]chemistry.harvard.edu" To: CCL Subject: CCL:G: AIM for molecular ion Message-Id: <-45720-111023192530-12156-H/eBGTQl/fxXe3WUD4zPsg _ server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 23 Oct 2011 19:25:08 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh-$-chemistry.harvard.edu] I made good experience with the 'Bader Charge Analysis' code (in DOS, i.e., you have to run it in the Win Command prompt): http://theory.cm.utexas.edu/bader/ Just produce a cube from your chk file (make sure that you have a grid which is dense enough for a converged AIM analysis!) and you are good to go: formchk your.chk your.fchk cubegen 0 density your.fchk your.density.cube -3 bader your.density.cube That's already it. Best Johannes ----------------------------------------------- Dr. Johannes Hachmann Postdoctoral Fellow Aspuru-Guzik Research Group Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Rm M104A Cambridge, MA 02138 USA eMail: jh**chemistry.harvard.edu ----------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh==chemistry.harvard.edu**ccl.net > [mailto:owner-chemistry+jh==chemistry.harvard.edu**ccl.net] On Behalf > Of Sergio Emanuel Galembeck segalemb__usp.br > Sent: Sunday, October 23, 2011 17:29 > To: Hachmann, Johannes > Subject: CCL:G: AIM for molecular ion > > > Sent to CCL by: Sergio Emanuel Galembeck [segalemb{=}usp.br] > Dear Dario, > > The use of AIM modules in Gaussian is not recommend, in part > because > this option is not maintained. I recommend the use of AIMAll, > because > this is a fast and robust program. > > Hope this help, > > Sergio > > > Citando "Dario Fernando Coral ferchocoralg16 .. gmail.com" > : > > > > > Sent to CCL by: "Dario Fernando Coral" [ferchocoralg16__gmail.com] > > regards > > > > Does anyone know how to perform AIM calculations in gaussian 09 or > > 03 for a molecular ion? > > > > I have performed this calculation for the neutral water molecule, > > but when I use AIM command on the furfuryl-aniline molecular ion, > > gaussian 09 has an error in the link L609 > > > > The route card I used is as follows: # ub3lyp/631g(d) AIM=charge > test > > > > thanks in advance> > > > > > > > > -= 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/ From owner-chemistry@ccl.net Sun Oct 23 20:10:00 2011 From: "A. Anglea a.anglea90[-]yahoo.com" To: CCL Subject: CCL: MP2 - hydrogen bond Message-Id: <-45721-111023200920-12257-8BGWz6bLCrYazSdRpU+21A{}server.ccl.net> X-Original-From: "A. Anglea" Date: Sun, 23 Oct 2011 20:09:17 -0400 Sent to CCL by: "A. Anglea" [a.anglea90~~yahoo.com] Hi all I am running potential energy scan in one dimension for hydrogen bond-complexes of water-Lewis bases at HF, DFT and MP2 levels, along Hydrogen bond axis. DFT and HF predict the correct order of hydrogen bond strength (according to the electron density on the Lewis bases). While, MP2 level doesn't. I tried to change the basis set for the Lewis base, but the results are the same. I used MP2(full), but again the results are the same. I was wondering, if there is any known problem with MP2 level to predict the hydrogen bond formed with water molecule. Any kind of help would be highly appreciated. Cheers From owner-chemistry@ccl.net Sun Oct 23 23:12:00 2011 From: "Emilio Xavier Esposito emilio.esposito:_:gmail.com" To: CCL Subject: CCL: COMP's San Diego ACS meeting abstract deadline: November 1st, 2011 Message-Id: <-45722-111023230211-14182-OuRVGla+UnjWOzBfzWcJqQ ~ server.ccl.net> X-Original-From: Emilio Xavier Esposito Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Sun, 23 Oct 2011 23:01:43 -0400 MIME-Version: 1.0 Sent to CCL by: Emilio Xavier Esposito [emilio.esposito%%gmail.com] Hi The COMP Programming Board would like to remind you that abstract submissions for the COMP technical meeting at the San Diego ACS meeting closes at 11pm Central Time on Tuesday, November 1st, 2011. Authors can submit their abstract at http://abstracts.acs.org . Information about the following COMP programming topics are listed below: - COMP Symposia at the San Diego ACS meeting - Graduate Student and Post Doc Image Contest - Organize a symposium within COMP at 2012 & 2013 ACS National Meeting Thank you for your time Emilio Xavier Esposito Michael Feig Maciej Haranczyk Melissa Landon Jeffry D Madura Eric V Patterson Yufeng Jane Tseng Scott A Wildman The COMP Programming Board http://web2011.acscomp.org/meetings/national-acs-program *COMP Symposia at the San Diego ACS meeting* Abstracts submitted to the Member Contributed COMP Symposia (oral) benefit from: - Each speaker is provided 30 minutes to present his or her work (25 minute talk and 5 minute Question and Answer session) - Talks on a common subject are presented together, providing the audience and speakers a cohesive experience The COMP Programming Board has expanded the Member Contributed presentation portion of the technical program for the San Diego ACS meeting to include the following: - Computational Approaches to Spectroscopy Analysis - Computational Study of Water - Data Science (Informatics) - Drug Discovery (ADME/Tox, Ligand-based, Methodology, & Target-base) - Materials Science - Membranes - Molecular Mechanics (Applications, Electrostatics & Polarization, Force Field Development, Methodology, and Proteins) - Quantum Chemistry (Applications, Methodology, and Quantum Dynamics & Monte Carlo Simulations) - Structural Bioinformatics - The COMP Poster Session The COMP technical program for San Diego can be found here: http://goo.gl/HJPSw and abstracts are to be submitted at http://absctracts.acs.org *Graduate Student and Post Doc Image Contest* One of the most powerful aspects of computational chemistry, biochemistry, and structural biology is the ability to create stunning images of our work. Our images are able to explain complex ideas and allow non-computational scientists the ability to understand our research. To highlight this aspect of the computational science, the COMP Division of ACS sponsors the Graduate Student and Post Doc Image Competition. More information and previous winners can be found here: http://web2011.acscomp.org/awards/brochureimagecontest _Criteria and Prize_ The COMP Programming Board will select the winning image and award the creator complimentary registration to a future ACS National Meeting, currently a $180 value for Graduate Students and a $360 value for Post Docs. The image must be created and submitted by a Graduate Student or Post Doc that is a member of the ACS and the COMP Division. Additionally, the image must be original work and cannot have been used in a previous publication (e.g., article image, Table of Contents image, or journal cover image). Images are due by 5pm Eastern Time on November 21st, 2011. Please email your image to Emilio Xavier Esposito ( emilio.esposito(0)gmail.com ). The image must be 3 inches wide by 4.5 inches tall, at least 300 dpi, and a PNG, EPS, JPEG, or PDF. Only one image per submitter. The creator of the winning image will be notified by email no later than Friday, December 16th, 2011. *Organize a symposium within COMP in 2012 or 2013* The COMP Programming Board is always looking for individuals that want to organize symposia and provides the framework and tools necessary to organize a great symposium. If you are interested in organizing a symposium for the 2012 national ACS meeting in Philadelphia (fall 2012) – or the 2013 national ACS meetings – please contact Emilio Xavier Esposito ( emilio.esposito(0)gmail.com ). This is an excellent opportunity for COMP’s members to organize symposia that are of interest to the scientific community. We are excited to receive your ideas for symposia.