From owner-chemistry@ccl.net Sat Feb 2 05:43:01 2008 From: "Abdeladim Guermoune lguermoune[A]hotmail.com" To: CCL Subject: CCL:G: problem with aim calculation Message-Id: <-36199-080202052911-17806-rlFVhj5HFNWX/QapXKUYuA##server.ccl.net> X-Original-From: "Abdeladim Guermoune" Date: Sat, 2 Feb 2008 05:29:07 -0500 Sent to CCL by: "Abdeladim Guermoune" [lguermoune#%#hotmail.com] Dear members, Its amazing to see how AIMALL program can generate easily the wfn file from formatted check file (Fchk) without problem usually encountered with Gaussian program. So I get the following results before treating the wfn data by aim2000. Bond ellipticity density Laplacian G V H (rho) (Del**2(rho( r)) Fe - B1 0,294 0,069 -0,014 0,023 -0,050 -0,027 Fe - H1 0,123 0,103 0,238 0,098 -0,137 -0,039 B2 - H1 0,391 0,101 -0,018 0,073 -0,151 -0,078 B1 - H2 0,280 0,117 0,156 0,131 -0,223 -0,092 B2 - H2 0,332 0,119 0,119 0,125 -0,220 -0,095 G : kinetic energy density. V : electronic potential energy H : the electronic density energy B: boron atom ; Fe : iron atom , H : hydrogen. Laplacian is calculated from formula: (-1/4 Del**2(rho( r)) as done in data file Its well known that Laplacian is related to the bond interaction energy by local expression of virial theorem. A positive value of Laplacian shows a depletion of electronic charge along the bond. This is the case in a closed-shell electrostatic interaction. A negative value of Laplacian, on the other hand, indicates that electronic charge is concentrated in the internuclear region. This is the case in an electron-sharing (or covalent) interaction. In this context, we expect to find : If the density is high , Laplacian will be negative. If the density is low , Laplacian will be positive. But as you can see above for the highest values of density correspond positive Laplacian. Can any expert in aim calculations tell me if I m wrong, or really some things is not correct with that file? Best regards; ----------------------------------- GUERMOUNE Abdeladim. University Cadi Ayyad Morocco. From owner-chemistry@ccl.net Sat Feb 2 07:55:00 2008 From: "abdeladim guermoune lguermoune\a/hotmail.com" To: CCL Subject: CCL:G: problem with aim calculation Message-Id: <-36200-080202075304-20900-pKOSwMJQ8w/jzq/xZm2oZA-x-server.ccl.net> X-Original-From: "abdeladim guermoune" Date: Sat, 2 Feb 2008 07:53:01 -0500 Sent to CCL by: "abdeladim guermoune" [lguermoune###hotmail.com] Dear members,Its amazing to see how AIMALL program can generate easily the wfn file from formatted check file (Fchk) without problem usually encountered with Gaussian program.So I get the following results before treating the wfn data by aim2000. Bond ellipticity rho Del**2(rho( r) G V H Fe - B1 0,294 0,069 -0,014 0,023 -0,050 -0,027 Fe - H1 0,123 0,103 0,238 0,098 -0,137 -0,039 B2 - H1 0,391 0,101 -0,018 0,073 -0,151 -0,078 B1 - H2 0,280 0,117 0,156 0,131 -0,223 -0,092 B2 - H2 0,332 0,119 0,119 0,125 -0,220 -0,095 Del**2(rho( r): Laplacian rho : density G : kinetic energy density. V : electronic potential energy H : the electronic density energy B: boron atom ; Fe : iron atom , H : hydrogen. Laplacian is calculated from formula: (-1/4 Del**2(rho( r)) as done in data file Its well known that Laplacian is related to the bond interaction energy by local expression of virial theorem. A positive value of Laplacian shows a depletion of electronic charge along the bond. This is the case in a closed-shell electrostatic interaction. A negative value of Laplacian, on the other hand, indicates that electronic charge is concentrated in the internuclear region. This is the case in an electron-sharing (or covalent) interaction. In this context, we expect to find :If the density is high , Laplacian will be negative.If the density is low , Laplacian will be positive. But as you can see above for the highest values of density correspond positive Laplacian.Can any expert in aim calculations tell me if I m wrong, or really some things is not correct with that file?Best regards; ----------------------------------- GUERMOUNE Abdeladim. University Cadi Ayyad Morocco. From owner-chemistry@ccl.net Sat Feb 2 10:08:00 2008 From: "Jeff Hammond jeff.science]|[gmail.com" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36201-080202100600-22686-DTtrD+KcA25SOtUczIMz/w!A!server.ccl.net> X-Original-From: "Jeff Hammond" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 2 Feb 2008 09:05:48 -0600 MIME-Version: 1.0 Sent to CCL by: "Jeff Hammond" [jeff.science#%#gmail.com] I am not affiliated with PNNL: I am not a lab employee, I live and work 2000 miles from the lab, and I've only even heard of one of the people you mentioned in your email. I develop code for NWChem as part my work in graduate school; that's it. I'm very sorry that my views have been misrepresented as having anything to do with PNNL's leadership. I greatly value the opportunities I have with NWChem while in graduate school and I sincerely hope that the false statements in your email do not jeopardize this. > 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. I have no goals about Gaussian. I said I personally do not need it - for scientific reasons or to compete with it - and what you're saying is not part of any mission, even my own. I'm not aware of any effort by anyone, anywhere to put Gaussian out of business deliberately. > 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. There isn't any basis for this in anything I've ever said in any forum or conversation. Anyways, I'm completely done with this business. Having negative statements about PNNL falsely attributed to me is not worth it, no matter how strongly I believe in an open source world. Peace, Jeff On Feb 1, 2008 10:07 PM, frisch[-]gaussian.com (Michael Frisch) wrote: > > 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> > > -- Jeff Hammond The University of Chicago From owner-chemistry@ccl.net Sat Feb 2 12:27:00 2008 From: "Nuno A. G. Bandeira nuno.bandeira+*+ist.utl.pt" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36202-080202120200-25114-jkocSp7FzhnnPvYKOlkFFQ:+:server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 02 Feb 2008 16:23:44 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira::ist.utl.pt] Jeff Hammond jeff.science{}gmail.com escreveu: > I have absolutely no need for Gaussian. I just believe in free, open > source software development as a matter of principle. Doesn't that sound a bit like fundamentalism ? Is you what you believe necessarily what others should abide by ? I've used crappy open source programs and crappy commercial programs. Neither side seems to gain or lose by their chosen method of licensing. -- 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 Sat Feb 2 13:49:00 2008 From: "Warren DeLano warren * delsci.com" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36203-080202134527-3577-OmW3bCUamkvS2Pm5JOKwkA*server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Sat, 2 Feb 2008 10:45:11 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren++delsci.com] Michael, > 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. For the record, it has been proven false that a company cannot provide source code, offer free versions of its software, and help its competitors enhance their own products while simultaneously enabling its employees to pay their mortgages and support their families. =20 The recent acquisitions of TrollTech (for $153M) and MySQL (for $1B) are just the latest examples of how it matters less and less whether one's code is open or one's licensing policy is restrictive and more and more whether one delivers total value to customers in ways which effectively entice them to keep coming back for more. Now, granted, if unique proprietary software capabilities are the only way in which a company can create and deliver value for its customers, then perhaps restrictive licensing and prohibitions on study and juxtaposition are warranted. But such approaches seem curiously out of place here in the sciences where most of us share a mission of helping humanity through open dissemination of our latest discoveries and techniques. =20 > ...snip... 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. Agreed. But such proprietary, unhelpful sentiment runs directly counter to the academic spirit of both academic science and of open-source software development, where we share most of our work, and we encourage others to extend and build upon it for the betterment of society. =20 Great companies need great business models, and freely giving away everything you create is no business model at all (though that didn't stop me from trying it for a while, just to be absolutely sure). But the opposite is also true: over-zealousness protection of intellectual property rights and licensing revenue is proven way to turn off customers and handicap your business. Balance is key. Citing the success DeLano Scientific LLC has had with PyMOL (an open-source product in the macro-molecular visualization market), I would challenge all scientific software companies which serve the chemical and biological research markets to identify and adopt business practices that are more in concert with the goals, approaches, and attitudes of their customers. It isn't just about open-source, free-source, or permissive licenses, though those can often help. It is fundamentally about understanding our shared scientific mission and finding ways to synergize and enable rather impede or prohibit. =20 (HINT: Whenever feasible, avoid license fees, lawyers, and the word "no"!) Cheers, Warren L. DeLano, Ph.D. Founder and Principal DeLano Scientific LLC DISCLAIMER: I have no specific knowledge of, experience with, or opinions regarding Gaussian, Inc. other than what I've read in the archives. I speak of and to the industry as a whole. Things have improved considerably over the past decade, but I still think we, collectively, can still do better for our scientific colleagues. PS. (from Michael's subsequent email) > Except that so far, enough people have felt that commercial quality=20 > 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=20 > the "free" software (more accurately, software paid for through taxes=20 > rather than license fees) is just as good, then we'll be out of=20 > business. That is a false dichotomy -- there are plenty examples of "commercial" scientific software originally developed at taxpayer expense in university settings and subsequently exploited by shrewd businesses. Likewise, there are now plenty of examples of free and/or open-source software creating through individual "hobby" efforts without a single cent of taxpayer support. "Commercial" quality software basically means that: (1) it installs quickly, easily, and reliably, (2) it does the job without crashing, (3) it is user friendly and comes with adequate documentation, (4) customers can call or email someone for help, (5) bugs get fixed reasonably quickly, and (6) some party is specifically accountable & liable for the software and doing everything they can to make you a happy customer. All of these things are important to customers, worth paying for, and can drive success in the software business. =20 Experience has convinced me that it is the lack of these things which keeps open-source software programs from displacing their proprietary alternatives, not the lack of a "proprietary" software license. From owner-chemistry@ccl.net Sat Feb 2 14:24:00 2008 From: "Serguei Patchkovskii Serguei.Patchkovskii#%#sympatico.ca" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36204-080202080200-23936-yhdQNg4IxEhWVa6CEtgGMg]^[server.ccl.net> X-Original-From: "Serguei Patchkovskii" Date: Sat, 2 Feb 2008 08:01:56 -0500 Sent to CCL by: "Serguei Patchkovskii" [Serguei.Patchkovskii ~~ sympatico.ca] On Fri, 1 Feb 2008, frisch[-]gaussian.com (Michael Frisch) wrote: > 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. Dr. Frisch, It is regrettable what you apparently believe what the business success of your company could only be achieved by taking freely from the scientific community you are not prepared to contribute to on the same terms. However, this is entirely your choice to make, and it is not really appropriate for anybody else to quarrel with it. Many people would believe what prohibiting some of the leading scientists and laboratories in the world from using your product is unethical, and will base some of their decisions and statements on this assessment. However, this is entirely their choice, and it is really not up to you to dispute it. Unfortunately, now you also choose to attack personal integrity of people who are not even a party to the discussion. If you would like to maintain some degree of credibility, I suggest you should apologize to the good folks at PNNL. Yours, Serguei Patchkovskii From owner-chemistry@ccl.net Sat Feb 2 14:59:00 2008 From: "Jim Kress ccl_nospam=kressworks.com" To: CCL Subject: CCL:G: PCGAMESS vs Gaussian03? Message-Id: <-36205-080201215332-7090-nqmQoTyoRs2cpFWeBFFaHw]|[server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 1 Feb 2008 21:06:03 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam*_*kressworks.com] I provided comparison between Gaussian performance and PC GAMESS performance. I was subsequently banned by Gaussian by means of their decision to charge me as a commercial entity for Gaussian 2003 rather than the Academic pricing I had previously been offered for G94 and G98. BTW, I am a private individual, not affiliated with any company, university or government agency. I used Gaussian for my own personal, noncommercial projects. However, in a real sense, I am beholding to Frisch et al at Gaussian for taking this position since it forced me to find and acquire superior software (like PCGAMESS, NWCHEM, etc.) which actually provide superior results to Gaussian and with better performance and support. Jim Kress > -----Original Message----- > From: Jeff Hammond jeff.science]![gmail.com > [mailto:owner-chemistry.:.ccl.net] > Sent: Friday, February 01, 2008 3:10 PM > To: Kress, Jim > Subject: CCL:G: PCGAMESS vs Gaussian03? > > > 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 > > > > -= 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/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > From owner-chemistry@ccl.net Sat Feb 2 16:05:00 2008 From: "frisch~!~gaussian.com (Michael Frisch)" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36206-080202160328-19584-luvy3thlPTXSyLK5jlw0Kg^server.ccl.net> X-Original-From: frisch|a|gaussian.com (Michael Frisch) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Sat, 2 Feb 2008 16:01:46 -0500 Mime-Version: 1.0 Sent to CCL by: frisch|,|gaussian.com (Michael Frisch) On Sat, Feb 02, 2008 at 10:45:11AM -0800, Warren DeLano warren * delsci.com wrote: > > > > ...snip... 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. > > Agreed. But such proprietary, unhelpful sentiment runs directly counter > to the academic spirit of both academic science and of open-source > software development, where we share most of our work, and we encourage > others to extend and build upon it for the betterment of society. > This is very unfair, considering that everything we do at Gaussian is published in the open literature and that many of our methods and algorithms have been implemented from the papers in other people's software. Our publishing meets all the traditional standards of disclosure, reproducability, etc. Unlike some other companies, we do not have secret parameters or proprietary models. There has never been a requirement that computational people share their code at all in order to meet the academic standards, and indeed many professors have groups which write their own code and don't share it with anyone, and they are not criticized for failing to meet academic standards. > Great companies need great business models, and freely giving away > everything you create is no business model at all (though that didn't > stop me from trying it for a while, just to be absolutely sure). But > the opposite is also true: over-zealousness protection of intellectual > property rights and licensing revenue is proven way to turn off > customers and handicap your business. Balance is key. > Agreed. Our view of the balance is to publish our methods and to license the software, including source code, but not to direct competitors. Gaussian is criticized far more for our policy than other companies who don't license source code at all or who have secret models are for theirs. > > > 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. > > That is a false dichotomy -- there are plenty examples of "commercial" > scientific software originally developed at taxpayer expense in > university settings and subsequently exploited by shrewd businesses. > Likewise, there are now plenty of examples of free and/or open-source > software creating through individual "hobby" efforts without a single > cent of taxpayer support. > I don't understand what dichotomy you're referring to. If people don't license our software, we don't get paid. If the implication is that people would pay us as consultants to develop our software while being unwilling to pay licnese fees to support the same activity, this is simply untrue, at least in our market. Development on all the major quantum chemistry codes is either paid for by license fees or paid for by tax dollars. There's no one doing substantial quantum chemistry software development, which is very time consuming, paid for primarily by consulting fees. > "Commercial" quality software basically means that: (1) it installs > quickly, easily, and reliably, (2) it does the job without crashing, (3) > it is user friendly and comes with adequate documentation, (4) customers > can call or email someone for help, (5) bugs get fixed reasonably > quickly, and (6) some party is specifically accountable & liable for the > software and doing everything they can to make you a happy customer. > All of these things are important to customers, worth paying for, and > can drive success in the software business. > > Experience has convinced me that it is the lack of these things which > keeps open-source software programs from displacing their proprietary > alternatives, not the lack of a "proprietary" software license. > I don't think that anyone claims that the license itself makes the software more desirable. The connection is that doing the things you list above is a lot of work and isn't particularly fun. That means that people don't want to do it as a hobby, but rather will do it only if they are paid for doing it. Generating the steady revenue required to pay people to do this things means either having license fees or substantial government support. Mike From owner-chemistry@ccl.net Sat Feb 2 16:40:00 2008 From: "Jim Kress ccl_nospam**kressworks.com" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36207-080202145548-11715-0G9GMabWqH2NXwIPQ/GM+g _ server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 2 Feb 2008 14:53:22 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam-x-kressworks.com] This note from Frisch is just another illustration of the arrogance and sophistry of the people at Gaussian. Jim Kress > -----Original Message----- > From: frisch[-]gaussian.com (Michael Frisch) > [mailto:owner-chemistry/./ccl.net] > Sent: Friday, February 01, 2008 11:08 PM > To: Kress, Jim > Subject: CCL:G: Licensing software to competitors > > > 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 > > > > -= 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 Sat Feb 2 17:59:00 2008 From: "Warren DeLano warren[a]delsci.com" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36208-080202173854-5779-mDvFBOEXVmT5zj6uaZrJJg,,server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Sat, 2 Feb 2008 14:38:39 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren=-=delsci.com] =20 > This is very unfair, considering that everything we do at=20 > Gaussian is published in the open literature and that many of=20 > our methods and algorithms have been implemented from the=20 > papers in other people's software. Our publishing meets all=20 > the traditional standards of disclosure, reproducability,=20 > etc. Unlike some other companies, we do not have secret=20 > parameters or proprietary models. =20 Publications about software, especially complex numeric codes, do not enable actual reproduction. It is not the same as publishing the actual source code itself. However, Gaussian should be applauded for making source code available, albeit under restrictive terms (as necessitated by their current business model). =20 > There has never been a=20 > requirement that computational people share their code at all=20 > in order to meet the academic standards, and indeed many=20 > professors have groups which write their own code and don't=20 > share it with anyone, and they are not criticized for failing=20 > to meet academic standards. Indeed. Not only should should professors be criticized for do so, but there are an increasing number of people who believe that release of source code under open-source terms should be a mandatory requirement for taxpayer-funded software development and for publication in academic journals. > If the implication is that people would pay us as consultants to=20 > develop our software while being unwilling to pay license=20 > fees to support the same activity, this is simply untrue, at=20 > least in our market. Development on all the major quantum=20 > chemistry codes is either paid for by license fees or paid=20 > for by tax dollars. =20 On that, we'll have to agree to disagree. But I submit there are now far too many successful, market-redefining software development efforts NOT funded by licensing revenue OR taxpayer dollars for any proprietary software company to feel smug and secure relying primarily upon licensing over the long haul. =20 There are now myriad opportunities for people to form "software" companies based on a comprehensive mix of software development, maintenance, support, and other software-related services combined with sparing and judicious reliance on paid licenses, where necessary, and where appropriate. > There's no one doing substantial quantum=20 > chemistry software development, which is very time consuming,=20 > paid for primarily by consulting fees. Yet. From owner-chemistry@ccl.net Sat Feb 2 18:34:01 2008 From: "Dominic Ryan dominic.ryan(~)comcast.net" To: CCL Subject: CCL:G: Licensing software to competitors Message-Id: <-36209-080202175951-9471-Pn/20sOIH/5Lzl7SEFR2oQ**server.ccl.net> X-Original-From: Dominic Ryan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 02 Feb 2008 17:26:20 -0500 MIME-Version: 1.0 Sent to CCL by: Dominic Ryan [dominic.ryan : comcast.net] Hi Mike, I applaud all attempts to create a product in our industry that is valued enough to sustain a business, such as Gaussian's. Nor do I have a problem, a priori, with refusing to sell a license for the product to anyone for the reasons stated, it is your prerogative. The fact that both open and closed source modes co-exist indicates that there is room for both and that each brings value to the table. That sounds like a net gain for this relatively small community of science. But as this is such a small community I would like to better understand the reasoning behind your policy of not allowing comparisons to be published between Gaussian's product and others. Or, if I am misstating your policy I'd welcome the correction. On the face of it this seems to fly in the face of science. Do any other commercial products, software or otherwise, have similar prohibitions on comparisons? Without knowing more about why, it also creates the impression that Gaussian fears comparison, which begs the question why? Is that because it is actually not as good as other products? I find that very hard to believe. It is because it is merely comparable and you think people will not see the value? Clearly many do see value, likely from support and guidance that commercial support makes possible. And so, could you please explain why you have adopted this policy? Dominic Ryan DRI frisch[A]gaussian.com (Michael Frisch) wrote: > 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 Sat Feb 2 23:12:00 2008 From: "Bruno Andrade bandradefsa/a\yahoo.com.br" To: CCL Subject: CCL: How to perform a protein MD in Gromacs, with solvent Message-Id: <-36210-080202221058-11963-QFUlcUN75T8SuYkR43Hxvg[]server.ccl.net> X-Original-From: "Bruno Andrade" Date: Sat, 2 Feb 2008 22:10:53 -0500 Sent to CCL by: "Bruno Andrade" [bandradefsa-$-yahoo.com.br] Hi there, I'm currently using gromacs program (as beginer), and I had some crashes in the calculations. I am trying to perform a MD using water as solvent, but in gromacs I could not found any option to use the solvent effect directly binded to the protein target, I just found the genbox option and using it, the program retuns me a crash message (system colapses with box, or something like "your system is probably not equilibrated"). Ps.: The system converges on the energy minimization, using option 6 force field. How can I perform it better? Thank you for you help. Bruno Andrade.