From owner-chemistry@ccl.net Fri Feb 1 01:03:01 2008 From: "Yangsoo Kim vsmember++gmail.com" To: CCL Subject: CCL:G: PCGAMESS vs Gussian03? Message-Id: <-36181-080201005911-9687-qs7eJe5ZisnjNn415rTyoA[*]server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 1 Feb 2008 12:30:24 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember[A]gmail.com] Dear All, Has anyone of you had a chance to compare the recent version of PCGAMESS 7.1.5 (http://classic.chem.msu.su/gran/gamess/) vs Gaussian03? PCGAMESS claims that it's been improved a lot in terms of calculation speed compared to the original GAMESS US. But it is hard to find the comparison between PCGAMESS and Gaussian03. I believe Gaussian03 has more functions and flexibility other than quantum calculations (integration, visualization, etc.) as it is a commercial product, but if we just want to perform pure quantum calculations (geometry optimization, energy corrections, frequency calculations) what would be the difference between the two applications in terms of performance, especially the calculation speed? I think the calculation results obtained from the two packages would be essentially the same, right? Any comment would be greatly appreciated. Yangsoo Kim From owner-chemistry@ccl.net Fri Feb 1 08:48:00 2008 From: "Sergio Emanuel Galembeck segalemb : usp.br" To: CCL Subject: CCL:G: PCGAMESS vs Gussian03? Message-Id: <-36182-080201082807-396-gJADWNu+w7lV7UmDzyF2rQ%%server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 01 Feb 2008 11:27:50 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb(_)usp.br] Dear Yangsoo, Comparisons between softwares are always very interesting, but GaussianXX license does not allow any comparisons with other programs. Best, Sergio Citando "Yangsoo Kim vsmember++gmail.com" : > > Sent to CCL by: "Yangsoo Kim" [vsmember[A]gmail.com] > Dear All, > > Has anyone of you had a chance to compare the recent version of PCGAMESS > 7.1.5 (http://classic.chem.msu.su/gran/gamess/) vs Gaussian03? PCGAMESS > claims that it's been improved a lot in terms of calculation speed compare= d > to the original GAMESS US. But it is hard to find the comparison between > PCGAMESS and Gaussian03. > > I believe Gaussian03 has more functions and flexibility other than quantum > calculations (integration, visualization, etc.) as it is a commercial > product, but if we just want to perform pure quantum calculations (geometr= y > optimization, energy corrections, frequency calculations) what would be th= e > difference between the two applications in terms of performance, especiall= y > the calculation speed? > > I think the calculation results obtained from the two packages would be > essentially the same, right? > > Any comment would be greatly appreciated. > > Yangsoo Kim > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > From owner-chemistry@ccl.net Fri Feb 1 10:22:01 2008 From: "sudha.srivastava,jiit.ac.in" To: CCL Subject: CCL:G: query gaussian03 severe error #2070 Message-Id: <-36183-080131063856-14905-IswKAodyLVcrj0lj7gdZkg---server.ccl.net> X-Original-From: sudha.srivastava a jiit.ac.in Content-type: text/plain; charset=us-ascii Date: Thu, 31 Jan 2008 16:03:53 +0530 MIME-Version: 1.0 Sent to CCL by: sudha.srivastava ~ jiit.ac.in Dear CCLers, I have optimized the structure of a molecule using DFT in gaussian03. While trying to optimze the geometry along with solvent (Default , water) I have this error reoccuring with a number of different calculations sometimes at the beginning sometimes after a day or so calculation time. ******************************************************************** Severe Error Message # 2070 The processing of the last link ended abnormally All processing has been aborted. ************************************************************************* I will be thankful if anyone can help me out. Sudha From owner-chemistry@ccl.net Fri Feb 1 10:56:01 2008 From: "Nuno A. G. Bandeira nuno.bandeira{}ist.utl.pt" To: CCL Subject: CCL:G: PCGAMESS vs Gaussian03? Message-Id: <-36184-080201103929-7545-pzYVOMTxrbtVkkD1ukl2+g=server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 01 Feb 2008 14:42:01 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira]![ist.utl.pt] Sergio Emanuel Galembeck segalemb : usp.br escreveu: > > Sent to CCL by: Sergio Emanuel Galembeck [segalemb(_)usp.br] > Dear Yangsoo, > > Comparisons between softwares are always very interesting, but > GaussianXX license does not allow any comparisons with other > programs. It's funny because when Gaussian produces an output file, you can read the licensing terms under which you are allowed to use the program and I honestly could never find that clause. The closest thing I can find is: "This program may not be used in any manner that competes with the business of Gaussian, Inc." but when you run hardware performance testing you're not competing with the program. In fact many research groups, like my own, use more than one software for research so it's more than likely that performance testing has been done with G03 vis-à-vis other programs. From what I can gather only software developers (and therefore competitors) are forbidden to access the source code for obvious reasons. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student __ IST,Lisbon -- From owner-chemistry@ccl.net Fri Feb 1 12:24:00 2008 From: "Aniko Simon aniko%x%simbiosys.ca" To: CCL Subject: CCL: Freeware for protein-small molecule minimization Message-Id: <-36185-080201121103-4675-+gEolFXpKDC4Q7iroNOiTg*server.ccl.net> X-Original-From: "Aniko Simon" Date: Fri, 1 Feb 2008 12:11:00 -0500 Sent to CCL by: "Aniko Simon" [aniko_._simbiosys.ca] Hi Manali, The eHiTS Score utility, which is available free of charge for academic researchers, has the option to perform an optimization of the ligand within the constraints of the receptor. The positioning of the flexible hydrogens on the receptor is also optimized. eHiTS Score is very easy to use and will generate results very rapidly. To obtain a copy of eHiTS Score, please visit the following link and request a demo of eHiTS: http://www.simbiosys.ca/products/demo_request.html I hope this will met your needs. Aniko Manali Joshi manali%%adrik.bchs.uh.edu wrote: > Sent to CCL by: "Manali Joshi" [manali**adrik.bchs.uh.edu] > Hi, > > I have a protein and a list of thousands of small molecules in the appropriate binding orientation. I want to be able to perform energy minimization of the binding site of the protein with each small molecule (using semi-empirical or similar charges). > I am looking for freeware that can automate this process. > Any help will be greatly appreciated. > > Thanks > Manali From owner-chemistry@ccl.net Fri Feb 1 13:06:01 2008 From: "perico^stark.udg.es" To: CCL Subject: CCL: VIII Girona Seminar on Aromaticity: basics and applications Message-Id: <-36186-080201123609-10887-rd8ELvMq2lQkuN0FHuevVQ[*]server.ccl.net> X-Original-From: perico#%#stark.udg.es Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 1 Feb 2008 18:35:56 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: perico%%stark.udg.es VIII Girona Seminar on Aromaticity: Basics and Applications Girona (Catalonia, Spain), 7-10 July 2008 Scope The Girona Seminars have been taken place in the historic town of Girona every two years since back to 1993, with the aim of bringing together, in a beautiful environment and in an informal and friendly atmosphere, young and senior scientists. The forthcoming VIII edition will be specially devoted to the recent developments and applications of Quantum Chemistry for the analysis and quantification of one of the most controversial classical concepts of chemistry: the aromaticity. Furthermore, following the tradition of this conference, other aspects of Quantum, Theoretical and Mathematical Chemistry such as Density Functional Theory, Electron Distribution and Chemical Bonding, or Photochemistry will be covered as well. Conference Organizers Prof. Dr. Ramon Carbo-Dorca Chairman of the Local Organizing Committee Prof. Dr. Miquel Sola Chairman assistant of the Local organizing Comitee Prof. Dr. Miquel Duran Secretary of the Local organizing Comitee Dr. Pedro Salvador Secretary assistant of the Local organizing Comitee International Advisory Board Juan Andres (Spain) Evert Jan Baerends (The Netherlands) F. Matthias Bickelhaupt (The Netherlands) Alexander I. Boldyrev (USA) Patrick Bultinck (Belgium) Jerzy Cioslowski (Poland) David Cooper (United Kingdom) Patrick W. Fowler (United Kingdom) Gernot Frenking (Germany) T. Marek Krygowsdi (Poland) Fernando Martin (Spain) Istvan Mayer (Hungary) Robert Ponec (Czech Republic) Paul von Rague Schleyer (USA) Jesus Ugalde (Spain) Keynote lecturers (in alphabetic order) Andres, Juan (Universitat Jaume I, Spain) Ayers, Paul W. (McMaster University, Canada) Baerends, Evert-Jan (Vrije Universiteit, Amsterdam) Bickelhaupt, Matthias (Vrije Universiteit, Amsterdam) Boldyrev, Alexander (Utah State University, USA) Bultnick, Patrick (University of Ghent, Belgium) Carbo-Dorca, Ramon (Universitat de Girona (Spain) and Ghent University (Belgium)) Cioslowski, Jerzy (University of Szczecin, Poland) Clark, Aurora E. (Washington State University, USA) Cooper, David (University of Liverpool, United Kingdom) Corminboeuf, Clemence (Ecole Polytechnique Federal de Lausanne, Switzerland) Cossio, Fernando (Donostiako Kimika Fakultatea, Spain) Deumal, Merce (Universitat de Barcelona, Spain) Fowler, Patrick W. (University of Sheffield, UK) Frenking, Gernot (Philipps-Universitaet Marburg, Germany) Galembeck, Sergio (Universidade de Sao Paulo, Brazil) Geerlings, Paul (Vrije Universiteit Brussel, Belgium) Havenith, Remco (Uttrecht University, The Netherlands) Krygowski, Marek (University of Warsaw, Poland) Mandado, Marcos (Universidad de Vigo, Spain) Martin, Fernando (Universidad Autonoma de Madrid, Spain) Martin-Pendas, Angel (Universidad de Oviedo, Spain) Matta, Cherif (Mount Saint Vincent University, Halifax, Canada) Mayer, Istvan (Hungarian Academy of Sciences, Hungary) Merino, Gabriel (Universidad de Guanajuato, Mexico) Palusiak, Marcin (University of Lodz, Poland) Piris, Mario (Euskal Herriko Unibertsitatea, Spain) Ponec, Robert (Czech Academy of Sciences, Czech Republic) Popelier, Paul (University of Manchester, UK) Ruedenberg, Klaus (Iowa State University, USA) Schleyer, Paul V. R. (University of Georgia, USA) Schwarz, W. H. Eugen (Universitaet Siegen, Germany) Shishkin, Oleg (National Academy of Sciences of Ukraine, Ukraine) Soncini, Alessandro (Katholieke Universiteit Leuven, Belgium) Tsipis, Constantinos (Aristotle University of Thessaloniki, Greece) Ugalde, Jesus (Euskal Herriko Unibertsitatea, Spain) Zanasi, Ricardo (University of Salerno, Italy) Prices - Regular Registration fee: 325 euro Includes: Admission to all scientific sessions, conference material, coffee breaks, lunches and Conference dinner. - PhD Students fellowship Registration fee: 175 euro (10 positions available upon application). Important Deadlines - Pre-registration form and Fellowship application: March, 30th - Registration Form, Booking Accomodation and Registration Payment: May, 18th - Abstract Submission: June, 1st Please visit the following URL for further information and pre-registration: http://iqc.udg.edu/gsaba2008 We are looking forward to seeing you in Girona, The Organizing Committee From owner-chemistry@ccl.net Fri Feb 1 13:41:00 2008 From: "Paulo Abreu qtabreu#,#ci.uc.pt" To: CCL Subject: CCL:G: PCGAMESS vs Gaussian03? Message-Id: <-36187-080201130510-27574-jkocSp7FzhnnPvYKOlkFFQ|-|server.ccl.net> X-Original-From: "Paulo Abreu" Content-Type: multipart/alternative; boundary="----=_Part_24493_14604579.1201889092999" Date: Fri, 1 Feb 2008 18:04:52 +0000 MIME-Version: 1.0 Sent to CCL by: "Paulo Abreu" [qtabreu|-|ci.uc.pt] ------=_Part_24493_14604579.1201889092999 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello Not wanting to ignite a debate on this subject (I am not a gaussian user) I quote from http://www.bannedbygaussian.org/ " "Further, under no circumstances will LICENSEE quote any performance data to third parties except with respect to the Software as delivered to LICENSEE."" I dont know if this is true because I dont have access to the program in question. Regards P. E. Abreu ------=_Part_24493_14604579.1201889092999 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello
Not wanting to ignite a debate on this subject (I am not a gaussian user) I quote from http://www.bannedbygaussian.org/
" "Further, under no circumstances will LICENSEE quote any performance data to third parties except with respect to the Software as delivered to LICENSEE.""
I dont know if this is true because I dont have access to the program in question.

Regards
P. E. Abreu


------=_Part_24493_14604579.1201889092999-- From owner-chemistry@ccl.net Fri Feb 1 14:15:00 2008 From: "Paulo E. Abreu paulo.abreu[A]ci.uc.pt" To: CCL Subject: CCL:G: PCGAMESS vs Gaussian03? Message-Id: <-36188-080201121331-4868-69R5uKodRoFFeUDvsZByfw#,#server.ccl.net> X-Original-From: "Paulo E. Abreu" Content-Type: multipart/alternative; boundary="----=_Part_24238_21603876.1201884543829" Date: Fri, 1 Feb 2008 16:49:03 +0000 MIME-Version: 1.0 Sent to CCL by: "Paulo E. Abreu" [paulo.abreu|ci.uc.pt] ------=_Part_24238_21603876.1201884543829 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello Not wanting to ignite a debate on this subject (I am not a gaussian user) I quote from http://www.bannedbygaussian.org/ " "Further, under no circumstances will LICENSEE quote any performance data to third parties except with respect to the Software as delivered to LICENSEE."" I dont know if this is true because I dont have access to the program in question. Regards P. E. Abreu ------=_Part_24238_21603876.1201884543829 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello
Not wanting to ignite a debate on this subject (I am not a gaussian user) I quote from http://www.bannedbygaussian.org/
" "Further, under no circumstances will LICENSEE quote any performance data to third parties except with respect to the Software as delivered to LICENSEE.""
I dont know if this is true because I dont have access to the program in question.

Regards
P. E. Abreu
------=_Part_24238_21603876.1201884543829-- From owner-chemistry@ccl.net Fri Feb 1 14:50:01 2008 From: "Jim Kress ccl_nospam#%#kressworks.com" To: CCL Subject: CCL: Project molecular geometry into symmetry point group? Message-Id: <-36189-080131132216-12411-Cm8e+CG48w7nrJaEuJP3jg*o*server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 31 Jan 2008 12:37:17 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam+*+kressworks.com] Have you tried ChemCraft? www.chemcraftprog.com Jim > -----Original Message----- > From: Seth Olsen s.olsen1-*-uq.edu.au > [mailto:owner-chemistry++ccl.net] > Sent: Wednesday, January 30, 2008 10:47 PM > To: Kress, Jim > Subject: CCL: Project molecular geometry into symmetry point group? > > > Sent to CCL by: Seth Olsen [s.olsen1#%#uq.edu.au] > > Hi CCL'ers, > > I have a molecular geometry that is very close to C3 > symmetry, but apparently is not. The molecule is large, so > it is going to take a prohibitively long time to sort through > all the bonds, angles, etc. Can anyone point me to a > software package that I can use to project the geometry into > the right symmetry group? Even better would be a package > that also would tell me just how big the alteration is upon making it. > > Cheers, > > Seth > > -- > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > > Dr Seth Olsen, PhD > Postdoctoral Fellow, Biomolecular Modeling Group Centre for > Computational Molecular Science Australian Institute of > Bioengineering and Nanotechnology (75) The University of > Queensland Qld 4072, Brisbane, Australia > > tel (617) 3346 3976 > fax (617) 3365 4623 > email: s.olsen1|-|uq.edu.au > Web: www.ccms.uq.edu.au > > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > The opinions expressed here are my own and do not represent > the official position of the University of Queensland, its > trustees or subsidiaries. > > > > -= This is automatically added to each message by the mailing > script =- To 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.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > From owner-chemistry@ccl.net Fri Feb 1 15:29:01 2008 From: "Jeff Hammond jeff.science]![gmail.com" To: CCL Subject: CCL:G: PCGAMESS vs Gaussian03? Message-Id: <-36190-080201151038-21357-J8sQyehlgIG/Q78kxjONfw]-[server.ccl.net> X-Original-From: "Jeff Hammond" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 1 Feb 2008 14:10:24 -0600 MIME-Version: 1.0 Sent to CCL by: "Jeff Hammond" [jeff.science%gmail.com] Nuno, The license quoted in the output file is not complete. A recent (October 11th, 2006) Gaussian license (http://www.ace-net.ca/software/Gaussian_License.pdf) contains the following (item 6): "Subject to the restrictions set for the in this Agreement, LICENSEE may provide to third parties who are not directly or indirectly engaged in competition with GAUSSIAN and whose confidentiality obligations to LICENSEE include the Software, access to the binary code of the Software solely at LICENSEE's business address specified above and on computers referenced above in Paragraph 1 and owned, operated by, and under the supervision of LICENSEE at such address. LICENSEE may not provide or knowingly allow access to third parties in exchange for services, fees, royalties, payments, or any other consideration to LICENSEE, and any such access with be governed by a separated Agreement between GAUSSIAN and LICENSEE. LICENSEE will not permit third parties to use the Software as modified by LICENSEE. Further, under no circumstances will LICENSEE quote any performance data to third parties except with respect to the Software as delivered to LICENSEE." Any errors are mine; the original was a fax and transcription was difficult. Regarding another part of your email, I do not agree that there are any obvious reasons not give competitors access to source code ["From what I can gather only software developers (and therefore competitors) are forbidden to access the source code for obvious reasons."] I develop code for NWChem, yet have no problem licensing the source code for GAMESS, PSI, MPQC, Dalton, Aces or Columbus. Are all the authors of these codes oblivious to the reasons for preventing competitors from accessing either binaries or source? In at least one case, a lead developer has provided me with technical support on his program when I told him it was specifically to develop competing features. Dishonest effort has little point: copying source code from another program is almost always harder than writing it from scratch using the literature. In the rare case where copying code might make sense, a GPL or equivalently license version is usually available (BLAS/LAPACK/GSL/Boost). By the time someone figured out all the variable names and internal conventions of one those hideous all-caps Fortran77 quantum chemistry programs, an honest programmer would have his version up-and-running. For the parallel case, it is even worse. Trying to turn a good serial code into a good parallel code is rarely productive; numerous case studies (NWChem is but one) demonstrate that starting from scratch - both with code and the underlying algorithms - leads to better results. Finally, open-sourcing is a great way to minimize the technical support burden. I debug 99% of my job errors in the aforementioned programs just by reading the source code. Jeff On Feb 1, 2008 12:04 PM, Paulo Abreu qtabreu#,#ci.uc.pt wrote: > > Hello > Not wanting to ignite a debate on this subject (I am not a gaussian user) I > quote from http://www.bannedbygaussian.org/ > " "Further, under no circumstances will LICENSEE quote any performance data > to third parties except with respect to the Software as delivered to > LICENSEE."" > I dont know if this is true because I dont have access to the program in > question. > > Regards > P. E. Abreu > > > -- Jeff Hammond The University of Chicago From owner-chemistry@ccl.net Fri Feb 1 16:30:00 2008 From: "N. Sukumar nagams#rpi.edu" To: CCL Subject: CCL:G: PCGAMESS vs Gaussian03? Message-Id: <-36191-080201162623-4899-ApsVT/Yx4yRHvzxDW26gpQ..server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Fri, 01 Feb 2008 16:26:11 -0500 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams__rpi.edu] Looks like the next round of the Gaussian wars have started in earnest! I just want to remark about "those hideous all-caps Fortran77 quantum chemistry programs," converting all-caps into lower case or sentence case is as trivial as the click of a button in most text editors today or a single command in a Unix shell. Amazing what some folks can get hung up over! N. Sukumar Associate Research Professor of Chemistry and Chemical Biology Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute http://reccr.chem.rpi.edu/ ==============Original message text=============== On Fri, 01 Feb 2008 15:10:24 EST "Jeff Hammond jeff.science]![gmail.com" wrote: Sent to CCL by: "Jeff Hammond" [jeff.science%gmail.com] Nuno, The license quoted in the output file is not complete. A recent (October 11th, 2006) Gaussian license (http://www.ace-net.ca/software/Gaussian_License.pdf) contains thefollowing (item 6): "Subject to the restrictions set for the in this Agreement, LICENSEE may provide to third parties who are not directly or indirectly engaged in competition with GAUSSIAN and whose confidentiality obligations to LICENSEE include the Software, access to the binary code of the Software solely at LICENSEE's business address specified above and on computers referenced above in Paragraph 1 and owned, operated by, and under the supervision of LICENSEE at such address. LICENSEE may not provide or knowingly allow access to third parties in exchange for services, fees, royalties, payments, or any other consideration to LICENSEE, and any such access with be governed by a separated Agreement between GAUSSIAN and LICENSEE. LICENSEE will not permit third parties to use the Software as modified by LICENSEE. Further, under no circumstances will LICENSEE quote any performance data to third parties except with respect to the Software as delivered to LICENSEE." Any errors are mine; the original was a fax and transcription was difficult. Regarding another part of your email, I do not agree that there are any obvious reasons not give competitors access to source code ["From what I can gather only software developers (and therefore competitors) are forbidden to access the source code for obvious reasons."] I develop code for NWChem, yet have no problem licensing the source code for GAMESS, PSI, MPQC, Dalton, Aces or Columbus. Are all the authors of these codes oblivious to the reasons for preventing competitors from accessing either binaries or source? In at least one case, a lead developer has provided me with technical support on his program when I told him it was specifically to develop competing features. Dishonest effort has little point: copying source code from another program is almost always harder than writing it from scratch using the literature. In the rare case where copying code might make sense, a GPL or equivalently license version is usually available (BLAS/LAPACK/GSL/Boost). By the time someone figured out all the variable names and internal conventions of one those hideous all-caps Fortran77 quantum chemistry programs, an honest programmer would have his version up-and-running. For the parallel case, it is even worse. Trying to turn a good serial code into a good parallel code is rarely productive; numerous case studies (NWChem is but one) demonstrate that starting from scratch - both with code and the underlying algorithms - leads to better results. Finally, open-sourcing is a great way to minimize the technical support burden. I debug 99% of my job errors in the aforementioned programs just by reading the source code. Jeff On Feb 1, 2008 12:04 PM, Paulo Abreu qtabreu#,#ci.uc.pt wrote: > > Hello > Not wanting to ignite a debate on this subject (I am not a gaussian user) I > quote from http://www.bannedbygaussian.org/> " "Further, under no circumstances will LICENSEE quote any performance data > to third parties except with respect to the Software as delivered to > LICENSEE."" > I dont know if this is true because I dont have access to the program in > question. > > Regards > P. E. Abreu > > > -- Jeff Hammond The University of Chicagohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Fri Feb 1 18:48:00 2008 From: "Kemi A Oloba ooloba ~ uh.edu" To: CCL Subject: CCL: NBO error Message-Id: <-36192-080201180819-6411-wRVe8VpVubvLUsgdRUDTVw++server.ccl.net> X-Original-From: "Kemi A Oloba" Date: Fri, 1 Feb 2008 18:08:16 -0500 Sent to CCL by: "Kemi A Oloba" [ooloba-,-uh.edu] I am trying to run a NBO job and keep getting this error. pls can someone help me thanks From owner-chemistry@ccl.net Fri Feb 1 19:23:00 2008 From: "Kemi A Oloba ooloba]![uh.edu" To: CCL Subject: CCL: NBO error Message-Id: <-36193-080201175243-5304-ojeTGSJ58dQiffzb3z0E2Q.@.server.ccl.net> X-Original-From: "Kemi A Oloba" Date: Fri, 1 Feb 2008 17:52:40 -0500 Sent to CCL by: "Kemi A Oloba" [ooloba-x-uh.edu] I am trying to run a NBO job and keep getting this error. pls can someone help me thanks From owner-chemistry@ccl.net Fri Feb 1 19:57:00 2008 From: "Eve G Zoebisch eve%x%ripariansoftware.com" To: CCL Subject: CCL:G: PCGAMESS vs Gussian03? Message-Id: <-36194-080201184506-8862-mDNFcwQC/VKkPqH+CA4kDQ[]server.ccl.net> X-Original-From: "Eve G Zoebisch" Date: Fri, 1 Feb 2008 18:45:02 -0500 Sent to CCL by: "Eve G Zoebisch" [eve() ripariansoftware.com] I took a class in Intellectual Property Law at Stanford and the course included Unfair Competition Law. As I recall, consumers have a legal right to compare products (i.e. they have a legal right to run benchmarks for competing products) and they had a right to distribute the results to other customers. My reading of the Gaussian license agreement is that Gaussian does not want individuals to modify the Gaussian code and publish the benchmark of the MODIFIED code since this would not be a fair comparison. Note: I am not a Gaussian customer and have not read the full license agreement, only the portion provided in earlier CCL messages. From owner-chemistry@ccl.net Fri Feb 1 21:22:01 2008 From: "frisch[A]gaussian.com (Michael Frisch)" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36195-080201201503-32102-Au/qAxHII6T7fQd6R7/4Ng*server.ccl.net> X-Original-From: frisch%a%gaussian.com (Michael Frisch) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 1 Feb 2008 19:41:39 -0500 Mime-Version: 1.0 Sent to CCL by: frisch!A!gaussian.com (Michael Frisch) > Sent to CCL by: "Jeff Hammond" [jeff.science%gmail.com] > Nuno, > > I develop code for NWChem, yet have no problem licensing the source > code for GAMESS, PSI, MPQC, Dalton, Aces or Columbus. Are all the > authors of these codes oblivious to the reasons for preventing > competitors from accessing either binaries or source? In at least one > case, a lead developer has provided me with technical support on his > program when I told him it was specifically to develop competing > features. > Interestingly, the primary authors of all these programs are either government employees or tenured faculty at universities. None of them depend on revenue from licensing their software in order to pay their mortgages and support their families, in contrast to the people working here at Gaussian. For that matter, I notice that you didn't mention receiving source code from Schroedinger, Wavefunction, or Q-Chem, either. As for binaries, I don't know how you spend your time, but here we end up working pretty hard to make sure that a new model or method is both formally correct and correctly implemented when there are no known correct answers to compare with. Implementing something already done by someone else is much easier given right answers for comparision, and easier still given printout of the intermediate quantities in the calculation. Both of these are available from binary versions of a program. You have every right to implement something I've done, but I have no obligation to help you do it with less work than it took me by providing you with a debugging tool. There's probably more money spent on NWChem development every year than Gaussian, Inc. has had to spend in its entire 20-year existence. The justification for spending all this government money was that existing codes could not meet the needs of PNNL. After more than a decade of development at this level of funding, focused on the specific needs of the laboratory, how could you possibly have any need for what we've done here with far more limited resources and without any particular emphasis on PNNL's needs? Mike Frisch From owner-chemistry@ccl.net Fri Feb 1 22:15:01 2008 From: "Jeff Hammond jeff.science{}gmail.com" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36196-080201221314-17696-85SrheIaI6XdYE4GVF//aA%server.ccl.net> X-Original-From: "Jeff Hammond" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 1 Feb 2008 21:13:04 -0600 MIME-Version: 1.0 Sent to CCL by: "Jeff Hammond" [jeff.science^_^gmail.com] I'm sorry that you have to pay your mortgage by selling something that others give away for free. That sounds likes an absolutely terrible business model. I have absolutely no need for Gaussian. I just believe in free, open source software development as a matter of principle. Jeff From owner-chemistry@ccl.net Fri Feb 1 22:49:00 2008 From: "Shunichi Ozawa s.ozawa/./infocom.co.jp" To: CCL Subject: CCL: INFOCOM releases ChemAxon's JChem nodes on KNIME workbench Message-Id: <-36197-080201203030-10969-IEObKlRrkFDcp/z+l+4gzw-x-server.ccl.net> X-Original-From: "Shunichi Ozawa" Date: Fri, 1 Feb 2008 20:30:26 -0500 Sent to CCL by: "Shunichi Ozawa" [s.ozawa%x%infocom.co.jp] JChem Extensions released: INFOCOM releases ChemAxon's JChem nodes on KNIME workbench Tokyo, Japan & Budapest, Hungary, January 31st, 2008 INFOCOM Corporation (http://www.infocom.co.jp/bio), a ChemAxon Integration Partner, today launched JChem Extensions for KNIME, which allows researchers to deal with chemical structure data using ChemAxons software tools such as Marvin, JChem, Standardizer, on the KNIME open source workflow platform. http://www.infocom.co.jp/bio/develop/jchemextension_en.html JChem Extensions offers a set of new KNIME nodes with which users can easily build their own workflows and data mining applications for working with chemical data. Further enhancing the use of the JChem Extensions, KNIME enables users to integrate their own software developed in house and other commercially available software tools such as those from Schrdinger or Tripos. JChem Extensions contains has about 20 novel nodes for the KNIME workflow platform, from basic functions dealing with chemical structure data (Basic module) to special functions using ChemAxons software tools such as Marvin, JChem, Standardizer and more. The development has been driven by our clients interest in ChemAxon and KNIME and the functionality we are launching is as a result of speaking to and testing with pharmaceutical researchers. For academic customer, INFOCOM offer JChem Extensions: Base without charge. Please see the following pages. ChemAxon's Academic Package sign up/more information page "http://www.chemaxon.com/acpack_conditions.html" JChem ExtensionsAcademic Package page http://www.infocom.co.jp/bio/develop/jchemextension_academic_en.html =================================================== Shunichi OZAWA (s.ozawa],[infocom.co.jp) Science Group Chem & Bio Informatics Department INFOCOM CORPORATION e-mail: info-science],[infocom.co.jp http://www.infocom.co.jp/index_e.html From owner-chemistry@ccl.net Fri Feb 1 23:24:01 2008 From: "frisch[-]gaussian.com (Michael Frisch)" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36198-080201230929-18667-TmeIFw7c5XdPzSXVZhdWPw .. server.ccl.net> X-Original-From: frisch^^^gaussian.com (Michael Frisch) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 1 Feb 2008 23:07:47 -0500 Mime-Version: 1.0 Sent to CCL by: frisch%x%gaussian.com (Michael Frisch) On Fri, Feb 01, 2008 at 09:13:04PM -0600, Jeff Hammond jeff.science{}gmail.com wrote: > > Sent to CCL by: "Jeff Hammond" [jeff.science^_^gmail.com] > I'm sorry that you have to pay your mortgage by selling something that > others give away for free. That sounds likes an absolutely terrible > business model. > > I have absolutely no need for Gaussian. I just believe in free, open > source software development as a matter of principle. > Except that so far, enough people have felt that commercial quality software was worth the price that we still have jobs, as do the people at the other software vendors in our market. If people decide that the "free" software (more accurately, software paid for through taxes rather than license fees) is just as good, then we'll be out of business. I'm glad that you acknowledge that this is your goal and that you don't need our software for any PNNL lab mission other than the one of putting us out of business. That removes any confusion about why PNNL asked to license our software, and illustrates our reasons for offering PNNL a license for use by everyone there except NWChem developers. PNNL turned down this license on the grounds that the NWChem developers were the ones who needed the license, which is also consistent with your goal. It is, however, inconsistent with what we were told by other people at PNNL (such as Doug Ray and Bruce Garrett), who originally said that PNNL wanted to use our software for application calculations related to lab missions and not as an aid in software development. Thank you for the clear confirmation that your managers were being less than honest with us concerning the goals and priorities of the laboratory. Mike