From owner-chemistry@ccl.net Tue Oct 25 04:12:01 2005 From: "Ding Xunlei dxl^^^ustc.edu.cn" To: CCL Subject: CCL: calculation on C60 using DMol3 Message-Id: <-29719-051024233121-27481-61ExEcgEI6Yy2M6+alOZKA|a|server.ccl.net> X-Original-From: "Ding Xunlei" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Tue, 25 Oct 2005 11:31:02 +0800 Mime-Version: 1.0 Sent to CCL by: "Ding Xunlei" [dxl%%ustc.edu.cn] Dear CCLs, I get an error when I do an energy calculation on C60 with DMol3, using dnd basis set and set "symmetry on"( C60 has Ih symmetry). The message is below: "Point group symmetry ih symmetry orbital prototypes generated (SYMDEC) Too many coefficients procof **** in T1U.1 Message: DMol3 job failed Error: DMol3 exiting" If set "symmetry off" or use dn basis set, the calculation is successful. Then how can I do the calculation with symmetry on and dnd basis set? Thank you! Yours sincerely, Ding Xunlei 2005-10-25 ______________________________________________ From owner-chemistry@ccl.net Tue Oct 25 05:03:00 2005 From: "Van Dam, HJJ \(Huub\) h.j.j.vandam|*|dl.ac.uk" To: CCL Subject: CCL: W:Calculation of Point Group Message-Id: <-29720-051025050013-9190-eSc6C2yCCSce8pLLLmWjCA],[server.ccl.net> X-Original-From: "Van Dam, HJJ \(Huub\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 25 Oct 2005 09:24:57 +0100 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam===dl.ac.uk] Hi, Are you running this from the windows command prompt or are you double clicking it? Huub -----Original Message----- > From: owner-chemistry*_*ccl.net [mailto:owner-chemistry*_*ccl.net] Sent: 24 October 2005 19:34 To: Vandam, Huub Subject: CCL: W:Calculation of Point Group Hi Serguei, i went to the mentioned website and downloaded the symmetry.c file. i am using Bloodshed Dev C++ IDE, it can handle C files too. i build the file and execute but all it does is give a black command prompt box, just like we the one we get in WinXp. i don;t understand the mistake i am committing. further i thought probably the zip files would be the updated version but same thing happened. could you plz tell what is mistake i am making. thanks= From owner-chemistry@ccl.net Tue Oct 25 06:07:01 2005 From: "David Cornil cornildavid_._yahoo.fr" To: CCL Subject: CCL: W:MAKPOL?! Message-Id: <-29721-051025060616-4666-tj+775NnS7/RvPy7U9iqNg:-:server.ccl.net> X-Original-From: "David Cornil" Sent to CCL by: "David Cornil" [cornildavid,;,yahoo.fr] Hello all, We did calculation on stacks with different molecules to calculate the ratio between the total dipole moment of the stack by the number of molecules. But we can not increase the number of molecules because of the atoms number limitation in the Mopac package. Our purpose is to do a AM1 calculation on a stack composed by an "infinite" number of molecules. This can be done with the help of periodic conditions. We heard about the possibility of doing this with the MAKPOL program included in the Mopac package. The trick in this program is to define a cell unit and to define the directions (the vector(s)) in wich the cell is repeating. Execute MAKPOL just gives us a repetition of the unit cell but does not give a result of an AM1 calculation. Execute a AM1 calculation with the following keywords, atom coordinates and unit cell vectors mers=(3) AM1 1SCF GRADIENTS C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 1.388330 1 0.000000 0 0.000000 0 1 0 0 C 1.406220 1 119.267000 1 0.000000 0 2 1 0 C 1.404060 1 120.616510 1 -0.012470 1 3 2 1 C 1.390640 1 119.257700 1 0.006220 1 4 3 2 C 1.404270 1 120.757950 1 0.011770 1 1 2 3 H 1.102180 1 119.631660 1 -179.989580 1 1 2 3 H 1.103920 1 120.469820 1 179.991700 1 2 1 3 H 1.103860 1 120.330350 1 -179.994720 1 4 3 2 H 1.101150 1 119.006770 1 -179.999380 1 5 4 3 S 1.686630 1 116.640520 1 179.994790 1 6 1 2 H 1.322650 1 100.218760 1 179.985000 1 11 6 1 N 1.483870 1 119.687200 1 179.987820 1 3 2 1 O 1.202210 1 118.993250 1 0.043290 1 13 3 2 O 1.202430 1 118.960780 1 -179.955960 1 13 3 2 XX 4.000000 0 90.000000 0 90.000000 0 1 2 3 TV 4.000000 1 90.000000 1 90.000000 1 1 2 3 gives the dipole moment of the molecule included in our unit cell but when we change mers=(3) by mers=(100), the dipole moment does not change !!!!! Maybe we miss something, is there anybody can help us : - to use MAKPOL in a right way - to understand the problem with Mopac calculation here above - to find maybe an other way to do periodic condition with AM1 Hamiltonian Thank you in advance Cornil David Centre de recherche Materia Nova Service de chimie des matriaux nouveaux Mail : cornildavid]*[yahoo.fr From owner-chemistry@ccl.net Tue Oct 25 06:42:02 2005 From: "Noel O Boyle no228||cam.ac.uk" To: CCL Subject: CCL: Summary: Where can you publish articles on software? Message-Id: <-29722-051025062544-17808-6EcaXVDyVUTrvgKN6rN2Tg*_*server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 25 Oct 2005 11:25:32 +0100 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228,;,cam.ac.uk] Dear CCLers, My original question was: "Where can one publish articles on programs that are of general interest to computational chemists, but which do not contain new algorithms?" Thanks to all those that contributed to the very lively discussion that followed. There appear to be two journals in which it may be possible to publish: Computer Physics Communications, and Journal of Computational Chemistry. Off-topic a number of issues were raised, which make for interesting reading (see below). I don't want to prolong this topic, but few people addressed the effect on science of not encouraging chemists to share code (which is one of the side-effects of not encouraging publication). On this list, people often write in looking for free code - how long will people continue to share code if they cannot get any academic recognition for the time they spend on it? Here is the original email: ====================================================================== Dear CCLers, Where can one publish articles on programs that are of general interest to computational chemists, but which do not contain new algorithms? For example, I have a program that parses the output of the logfiles of certain computational chemistry programs, shows the progress of the calculation graphically and can convolute some spectra. I would say that this is of general interest (judging by the number of downloads), but I cannot figure out whether any journals would accept an article describing the software (which is freely available, and open source). Regards, Noel O'Boyle. (http://gausssum.sf.net is the program in question) ====================================================================== Replies: ====================================================================== Sent to CCL by: David van der Spoel [spoel_._xray.bmc.uu.se] On Tue, 2005-10-11 at 09:45 +0100, Noel O Boyle no228 ~~ cam.ac.uk wrote: > Sent to CCL by: "Noel O'Boyle" [no228]_[cam.ac.uk] > Dear CCLers, > > Where can one publish articles on programs that are of general interest > to computational chemists, but which do not contain new algorithms? Comp. Phys. Comm. does that. > > For example, I have a program that parses the output of the logfiles of > certain computational chemistry programs, shows the progress of the > calculation graphically and can convolute some spectra. I would say that > this is of general interest (judging by the number of downloads), but I > cannot figure out whether any journals would accept an article > describing the software (which is freely available, and open source). > > Regards, > Noel O'Boyle. > (http://gausssum.sf.net is the program in question)> > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel#,#xray.bmc.uu.se spoel#,#gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ====================================================================== Sent to CCL by: Sergio Emanuel Galembeck [segalemb%%usp.br] Noel, I suggest Journal of Computational Chemistry. Best regards, Sergio Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo Av Bandeirantes, 3900 Ribeirao Preto, SP Brasil ====================================================================== Sent to CCL by: Jonathan Brecher [jsb],[cambridgesoft.com] At 4:45 AM -0400 10/11/05, Noel O Boyle no228 ~~ cam.ac.uk wrote: >Where can one publish articles on programs that are of general interest >to computational chemists, but which do not contain new algorithms? > >For example, I have a program that parses the output of the logfiles of >certain computational chemistry programs, shows the progress of the >calculation graphically and can convolute some spectra. I would say that >this is of general interest (judging by the number of downloads), but I >cannot figure out whether any journals would accept an article >describing the software (which is freely available, and open source). JCIM (the former JCICS) is pretty flexible about accepting papers that describe new software. But *please* don't waste everyone's time if you're simply looking for publicity. Find something scientifically interesting to say, or don't say anything. I once reviewed a paper that spent most of a page describing the behavior of a program's About Box. That paper didn't exactly get high marks from me... Jonathan Brecher jsb/a\cambridgesoft.com ====================================================================== Sent to CCL by: "Konrad Hinsen" [khinsen(-)cea.fr] On Oct 11, 2005, at 10:45, Noel O Boyle no228 ~~ cam.ac.uk wrote: > Where can one publish articles on programs that are of general interest > to computational chemists, but which do not contain new algorithms? The Journal of Computational Chemistry has a section for articles describing programs, but I don't know what their criteria for acceptance are. There is also Computer Physics Communications, which has some chemistry-oriented contributions in spite of "physics" in the title. --------------------------------------------------------------------- Konrad Hinsen Laboratoire Lon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen+/-cea.fr ====================================================================== Sent to CCL by: Michel Petitjean [ptitjean . itodys.jussieu.fr] To: chemistry^^ccl.net Subject: CCL: Re: Where can you publish articles on software? This programme is surely useful, but the editors of research journals would probably not accept it for publication. If this kind of article is acceptable, I guess that many people would produce tons of technical programmes and have hundreds of papers in their CV, then apply for some full Professor position without having done any scientific research. Publishing programmes for computational chemistry (or other) means (a) creating an original algorithm, and (b) programming it, and (c) running it on suitable data of interest. Regrettably, numerous molecular modeling papers published on the basis of step (c) alone bear the same value that papers involving (a)+(b)+(c). Michel Petitjean, Email: petitjean^^itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean^^ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html ====================================================================== Sent to CCL by: "Noel O'Boyle" [no228:+:cam.ac.uk] On Tue, 2005-10-11 at 16:23 +0200, Michel Petitjean ptitjean-.-itodys.jussieu.fr wrote: > Sent to CCL by: Michel Petitjean [ptitjean . itodys.jussieu.fr] > To: chemistry^^ccl.net > Subject: CCL: Re: Where can you publish articles on software? > > This programme is surely useful, but the editors of research journals > would probably not accept it for publication. If this kind of article > is acceptable, I guess that many people would produce tons of technical > programmes This is exactly what I think *should* be encouraged! If we look at bioinformatics, the latest issue of "BMC Bioinformatics" has 7 software articles (this journal has an impact factor of 5.42); the latest issue of "Bioinformatics" has 9 'Application Notes' (this journal has an impact factor of 5.74). There is a real interest in useful software that can make it easier to do science. > and have hundreds of papers in their CV, then apply for > some full Professor position without having done any scientific research. I don't think this has happened in bioinformatics, but I understand your point. However, I think that the benefits to the community outweigh this possibility. > Publishing programmes for computational chemistry (or other) means > (a) creating an original algorithm, and (b) programming it, and (c) > running it on suitable data of interest. > > Regrettably, numerous molecular modeling papers published on the basis > of step (c) alone bear the same value that papers involving (a)+(b)+(c). So where is the encouragement for me to write software that can help other people? To deal with bug reports, feature requests, installation problems. (You are probably familiar with this also, with your software) In addition, science should involve building on someone else's work, not reinventing the wheel. Wouldn't it be better if authors made their code available so that others could use it? Otherwise every person who wants to do a particular type of charge analysis, for example, has to read the algorithm, write the code, and get their result. During my PhD I found this to be the case for Hirshfeld Population Analysis. I spent a week and a half reinventing the wheel (and not very well). This is why I would like to be able to publish an article on a program. Regards, Noel ====================================================================== Sent to CCL by: "Perry E. Metzger" [perry++piermont.com] "Noel O'Boyle" writes: >> >> This programme is surely useful, but the editors of research journals >> would probably not accept it for publication. If this kind of article >> is acceptable, I guess that many people would produce tons of technical >> programmes > > This is exactly what I think *should* be encouraged! Yup... >> Publishing programmes for computational chemistry (or other) means >> (a) creating an original algorithm, and (b) programming it, and (c) >> running it on suitable data of interest. >> >> Regrettably, numerous molecular modeling papers published on the basis >> of step (c) alone bear the same value that papers involving (a)+(b)+(c). > So where is the encouragement for me to write software that can help > other people? To deal with bug reports, feature requests, installation > problems. (You are probably familiar with this also, with your software) > > In addition, science should involve building on someone else's work, not > reinventing the wheel. Wouldn't it be better if authors made their code > available so that others could use it? Otherwise every person who wants > to do a particular type of charge analysis, for example, has to read the > algorithm, write the code, and get their result. During my PhD I found > this to be the case for Hirshfeld Population Analysis. I spent a week > and a half reinventing the wheel (and not very well). > > This is why I would like to be able to publish an article on a program. Everything you say here makes sense. Science cannot progress on the attitude that tool building is an unimportant activity (it is not) or if we discourage tool building, or if we treat our tools as though sharing them with others would somehow be negative instead of an unmitigated positive thing. One great thing about open source (and I mean real open source, not the pseudo-open source that frequently is found in the Computational Chemistry world) is that it can be built on and everyone can share in the benefits of the improvements, just as we all share in the body of ideas that is science and try to contribute back so that the knowledge base increases. (When I say "pseudo-open", I mean the typical "you can use this for free but only if you send us a letter in triplicate, and don't dare alter it or publish the altered code". What is interesting about open source is *not* the price of the code -- it is the freedom to take parts of it, or improve it, or rearrange it to fix new problems.) Perry ====================================================================== Sent to CCL by: "Andy Holder" [holdera%umkc.edu] In reply to: > This programme is surely useful, but the editors of research journals > would probably not accept it for publication. If this kind of article > is acceptable, I guess that many people would produce tons of technical > programmes >>This is exactly what I think *should* be encouraged! If we look at >>bioinformatics, the latest issue of "BMC Bioinformatics" has 7 >>software articles (this journal has an impact factor of 5.42); the >>latest issue of "Bioinformatics" has 9 'Application Notes' (this journal >>has an impact factor of 5.74). There is a real interest in useful >>software that can make it easier to do science. I am the editor of the Journal of Molecular Graphics and Modelling, and we specifically EXCLUDE program announcements/descriptions from our pages. Programs are not original research, but may be implementations of original research. Being a former member of the Dewar group, they certainly published a large number of papers on semiempirical methods, but never published any article on AMPAC itself. These programs were even run on just a few examples of "suitable data of interest"! The algorithm is perhaos worthy of publication, and the program can certainly be mentioned, but is not in and of itself worthy of the valuable space in a research journal. Comparison to various other journals with high impact factors is anecdotal at best. The data from JMGM indicate that our IF went DOWN when we included these item and has been steadily increasing since we eliminated them. But that could also have been for a number of other reasons. My 0.02. Regards, Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JJJJJJJJ MMM MMM GGG MMM MMM | ANDREW J. HOLDER JJ MM MM GG GG MM MM | Editor JJ MMM MMM GG MMM MMM |J. of Molclr Grphcs & Modelling JJ MM M MM GG GGGG MM M MM | Dept. of Chemistry JJ JJ MM M MM GG GG MM M MM | Univ. of Missouri-Kansas City JJ GGG | Kansas City, MO 64110 | holdera-$-umkc.edu Published by Elsevier Science | (816)235-2293 * (816)235-6543F -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ====================================================================== Sent to CCL by: jle [jle-.-theworld.com] On Oct 11, 2005, at 11:47 AM, Noel O Boyle no228^-^cam.ac.uk wrote: > > In addition, science should involve building on someone else's work, > not > reinventing the wheel. Wouldn't it be better if authors made their code > available so that others could use it? Otherwise every person who wants > to do a particular type of charge analysis, for example, has to read > the > algorithm, write the code, and get their result. During my PhD I found > this to be the case for Hirshfeld Population Analysis. I spent a week > and a half reinventing the wheel (and not very well). > > This is why I would like to be able to publish an article on a program. > Well, if what they want is done by a commercially available program, they can purchase and use it without concern (assuming most such programs, particularly in the QM field) are validated and tested well. Otherwise, they can make the code available under the suitable open- source license or as a binary distribution on a website and post pointers on places such as CCL. We're still quite a small community, so if something's good and available, it'll turn up, or be Google-able. Writing the code's actually the smallest about of work. Debugging it, validating it, maintaining it and possibly porting it are usually way more work :-). Joe Leonard jle]![theworld.com ====================================================================== Sent to CCL by: "Noel O'Boyle" [no228===cam.ac.uk] On Tue, 2005-10-11 at 19:52 -0400, jle jle^^theworld.com wrote: > Sent to CCL by: jle [jle-.-theworld.com] > > This is why I would like to be able to publish an article on a program. > > > Well, if what they want is done by a commercially available program, > they can purchase and use it without concern (assuming most such > programs, particularly in the QM field) are validated and tested well. Except that they are restricted to the features available within that program. For example, I used a well-known commercially-available package during my PhD - I was very happy with its performance in general, but when I wanted to do Morokuma decomposition I found that it wasn't implemented. It *is* implemented in another freely-available package, but that package wasn't able to converge the SCF. So what we have are several different programs (some free and open-source, and some commercially-available) which implement different subsets of useful algorithms, and which are not interoperable. > Otherwise, they can make the code available under the suitable open- > source license or as a binary distribution on a website and post > pointers > on places such as CCL. We're still quite a small community, so if > something's > good and available, it'll turn up, or be Google-able. My point is that this doesn't happen - authors do *not* make the code available, and so other scientists have to write it themselves (and not all computational chemists can program). > Writing the code's actually the smallest about of work. Debugging it, > validating it, maintaining it and possibly porting it are usually way > more > work :-). This is indeed true, and is part of the reason code is not released - people aren't willing to support it, because of the work involved. Regards, Noel ====================================================================== Sent to CCL by: "Warren DeLano" [warren(~)delsci.com] > Sent to CCL by: "Andy Holder" [holdera%umkc.edu] Ironically, JMGM editor Andy Holder offers compelling reasons for why developer-scientists should shift their attention away from closed-access journals like JMGM and toward peer-reviewed open-access/open-source venues that better serve the overall needs of the field. > I am the editor of the Journal of Molecular Graphics and Modelling, > and we specifically EXCLUDE program announcements/descriptions from > our pages. Programs are not original research, but may be > implementations of original research. This fails to acknowledge the critical enabling role of software in computational chemistry and conveys a shockingly dismissive view of the original research aspects of computer programs! To put it as politely as I can, I most vehemently disagree. Such comments insult and demean the creative efforts of those who might have otherwise considered publishing papers in JMGM. > The data from JMGM indicate that our IF went DOWN > when we included these item and has been steadily increasing since we > eliminated them. Effective running software is at least as impactful as algorithmic descriptions, if not more so. (We live in real buildings, not architectural plans; we travel by plane, not via designs of planes). "Impact Factor" (I.F.) in terms of follow-on citations has little relevance as a measure of impact for scientific software and especially so once usage becomes widespread (e.g. ChemDraw, RasMol, Excel, etc.). Speaking from personal experience, recognizable PyMOL images are now routinely found in Science, Nature, C&EN, and many other journals, but such usage is rarely cited. So what is PyMOL's impact factor? Zero! It has never been officially "published" per se, even though its source code has been published continuously on the internet since early 2000. > The algorithm is perhaps worthy of > publication, and the program can certainly be mentioned, but is not in > and of itself worthy of the valuable space in a research journal. Such comments reflect little "editorial" sympathy for the publish-or-perish plight faced by academic scientists who develop practical algorithms in the form of working software programs instead of abstract algorithms in the form of non-working descriptive publications. Without such publications, the impact of developer-scientists is invisible to tenure review committees and funding agencies. That is unfair to many scientists and damaging to the field as a whole since better research software is very much needed. Developer-scientists need to be appropriately recognized and rewarded through career advancement, and thus it is not by accident that so many talented scientific software developers have chosen the private sector over the academic world. The system of academic credit is largely broken with respect to creation of quality research software. While JMCM may indeed have a fine "editorial" policy on this matter, it is justified for the wrong reasons. Programs cannot truly be "published" in traditional journals because they are too complex to describe precisely in such venues. A standalone print article does not deliver reproducibility and verifiability with respect to research software. Thus, journal articles describing software do not meet fundamental requirements of the scientific method. The only way to publish software in a scientifically robust manner is to share source code, and that means publishing via the internet in an open-access/open-source fashion. Anything short of that amounts to issuing unproven claims based on limited empirical tests regarding what a given program allegedly does. What is that called outside of science? Advertising! And as such, I agree that it does not belong in a scientific journal. Either you publish software with source code and stand behind it, or you are blowing smoke and quite *literally* hiding something -- no matter how noble your intent. > Being a former member of the Dewar group, they certainly published a > large number of papers on semiempirical methods, but never published > any article on AMPAC itself. Such comments confirm the notion that research software developers are not recognized for the critical enabling contributions they make, and reveal just how incapable the old closed-access, print-journal publication system is of meeting current needs. So, go live fellow research software developers, go live! Bypass an inadequate and obsolete system, and instead pursue internet-based open-access/open-source publishing of your work. If you lead, the world will follow. http://www.plos.org , http://www.doaj.org , http://pubchem.ncbi.nlm.nih.gov , http://www.blueobelisk.org , http://www.chmoogle.com , http://www.sf.net , etc. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren%x%delsci.com ====================================================================== Sent to CCL by: John McKelvey [jmmckel]-[attglobal.net] Folks, Am I wrong on this: Didn't Tom Ziegler, or someone, publish a nice article on ADF a while ago? Gave a lot of insight to a very credible code!!! Cheers, John McKelvey ====================================================================== Sent to CCL by Marcel Swart: Yes, see: Chemistry with ADF G. te Velde, F.M. Bickelhaupt, E.J. Baerends, C. Fonseca Guerra, S.J.A. van Gisbergen, J.G. Snijders, T. Ziegler Journal of Computational Chemistry, Vol. 22, No. 9, 931-967 (2001) But that was on the scientific aspects of ADF, not merely the technical part. ====================================================================== Sent to CCL by: Per-Ola Norrby [pon-$-kemi.dtu.dk] Dear all, I would recommend finding an interesting application for your software, publish the application, and in the same publication, add the description of the program as supporting information. This will open up a large number of possible journals, you can still use the reference as a required one when using your software, and if you cannot find an interesting, chemistry-related application, it probably isn't worth publishing in a chemistry journal anyway. /Per-Ola -- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon]=[kemi.dtu.dk tel +45-45252123, fax +45-45933968 ====================================================================== Sent to CCL by: Michel Petitjean [ptitjean[-]itodys.jussieu.fr] To: chemistry;;ccl.net Subject: CCL: Re(2): Where can you publish articles on software? The programming step is often the longest and the most difficult step (includes intensive validation tests, not to be confused with the "tests on suitable data of scientific interest"). Most scientists have each morning excellent ideas about new concepts, algorithms, or methods, but after having tried to programme the stuff, the ideas may appear to be very difficult to be realized. Worse: anyone remembers the chief telling to the young scientist: please just do it, the idea is important, not the technical task. Then the young collaborator spends much time and fails, but the chief admits the incompetence of the collaborator rather than the misconception of the idea. Clearly, I mean here that the programming step has much value, and that a good algorithm bears his full value AFTER being implemented in a programme. Nevertheless, I share the views of JMGM editor Andy Holder. (Note: I produce myself softwares and frewares, and I am the editor in chief of an open access journal), You can spend weeks and months to produce complicated programmes of general interest, it does not mean that it should be published in a scientific journal. The task may be done by an undergraduate student in computer sciences, or by a team of experienced software developpers: we do not care. If the utility programme has value, you can do one of the following (not exclusive): - Add a section or an appendix in the manuscript to be submitted - Provide the programme as "supplementary material" to the editor - Sell the programme (documentation may mention your contribution) - Put it in open access (documentation may mention your contribution) - Find a job and earn money in a company producing scientific softwares But please not: - Publishing a paper containing only programming stuff. Even the computer scientists do not publish that, and consider that the programming step is strictly technical. If you need to produce a new text editor incorporating utility functions for computational chemists (e.g. advancerd handling molecular graphics displays), would you try to publish it ? If you need this product, you can ask to somebody which is insensitive to the publish-or-perish requirement. If you have to do the task yourself, good luck ! The real problem is that using programmes to get results is better recognized that producing algorithms and programmes, although this latter scientific task is often longer and more difficult (furthermore, it needs pluridisciplinarity). Progress will be made when software will have the same value than patents (but please NO software patent). Michel Petitjean Email: petitjean;;itodys.jussieu.fr Editor-in-Chief of Entropy entropy;;mdpi.org ITODYS (CNRS, UMR 7086) ptitjean;;ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://www.mdpi.net/entropy http://www.mdpi.org/entropy http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html ====================================================================== Sent to CCL by: "Konrad Hinsen" [khinsen]^[cea.fr] On 12.10.2005, at 11:42, Noel O Boyle no228*cam.ac.uk wrote: >> Well, if what they want is done by a commercially available program, >> they can purchase and use it without concern (assuming most such >> programs, particularly in the QM field) are validated and tested well. > > Except that they are restricted to the features available within that > program. For example, I used a well-known commercially-available package Plus they are not extensible. I think one needs to make a difference between software that is intimately related to one's research and software that fulfills generic roles that different readily available programs can occupy. For example, I need a lot of control over the software that runs my MD simulations, but I can live very well with the text editors and C compilers that the outside world provides me. For anyone doing research in computational science, lack of control over their essential software implies a sever limitation to scientific creativity. I know many scientists who do not calculate the quantities that they would like to look at but the quantities that their programs allow them to calculate, even when those quantities are not really adequate. This is one reason why I consider the current state of the art in scientific computing (not just in chemistry) unsatisfactory. Given that it is not feasible for every scientist to write his own complex software, but that everyone should be able to extend and modify it, code quality, in particular readability and modularity, needs to acquire a much higher status than it has at the moment, and the education of computational scientists needs to include such elements as well as modern development techniques. > This is indeed true, and is part of the reason code is not released - > people aren't willing to support it, because of the work involved. That is indeed a significant problem which I am facing myself as well. But ultimately it is also a sign of the lack of recognition for the utility of scientific software development. In established and recognized aspects of research, support staff is considered an evident necessity. Hardly any lab chemist needs to argue for the necessity of having lab technicians (obtaining a position in a specific case if of course another matter). If software development were equally recognized, we would have programmer and support staff for big projects. -- ------------------------------------------------------------------------------- Konrad Hinsen Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen#%#cea.fr ------------------------------------------------------------------------------- ====================================================================== Sent to CCL by: "Konrad Hinsen" [khinsen!=!cea.fr] On Oct 13, 2005, at 11:29, Michel Petitjean ptitjean*|*itodys.jussieu.fr wrote: > But please not: > - Publishing a paper containing only programming stuff. > Even the computer scientists do not publish that, and consider that > the programming step is strictly technical. The same can be said for other aspects of research: as long as some work involves nothing but the straightforward application of known techniques, it should not be published in scientific journals. With occasional exceptions, that's what happens, thanks to the vigilance of editors and referees. However, a paper is not automatically strictly technical because its topic is a piece of software. If the design or the implementation of software involves new ideas that are of interest to the community, then it does in my opinion deserve publication in a scientific journal. In the case of complex applications, even the considerations that led the authors adopt one algorithm over another one can be sufficient to deserve publication, just as we see papers that compare different force fields. Here are a couple of papers on computational chemistry software that illustrate my point (pretty much an arbitrary selection from my paper collection): J. Comp. Chem. 18, 1848 (1997) J. Comp. Phys. 151, 283 (1999) J. Comp. Chem. 21, 79 (2000) J. Appl. Crystallography 37, 174 (2003) J. Comp. Chem. 24, 657 (2003) J. Comp. Chem. 26, 252 (2004) J. Comp. Chem. 26, 1647 (2005) None of them describes a straightforward implementation of known algorithms. I would wish that journal editors not refuse software-related papers as a matter of principle, but that they impose high standards for their evaluation. -- --------------------------------------------------------------------- Konrad Hinsen Laboratoire Lon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen.:.cea.fr --------------------------------------------------------------------- ====================================================================== Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci]_[UTMB.EDU] >>>You can spend weeks and months to produce complicated >>>programmes of general interest, it does not mean that >>>it should be published in a scientific journal. This misconception might explain why chemistry is well behind biology in terms of number of free software, Web servers, and databases. Software and database notes are regularly published in high-impact biology journals: Bioinformatics (Impact Factor=5.742), BMC Bioinformatics (IF=5.42), Nucleic Acids Research (IF=7.26). Each year, Nucleic Acids Research has a special issue for databases (see 2005 Database Issue, http://nar.oxfordjournals.org/content/vol33/suppl_1/index.dtl) and another one for Web servers (see Web Server Issue 2005, http://nar.oxfordjournals.org/content/vol33/suppl_2/index.dtl). Updates for databases (GenBank, PDB, SwissProt) or major bioinformatics software are regularly published, and the rule is to cite the most recent publication when using a database or a software (such as alignment tools, Web servers). The recent trend in computational biology is to move in areas traditionally belonging to computational chemistry. An example: NIH started PubChem, a database of organic compounds (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcsubstance). Very instructive was the answer from the American Chemical Society: ACS asked the Congress to cut the funding for PubChem, because it is a public project that competes with a private one (CAS). If the chemical community wants useful and free software, then it should accept papers on software. For the moment, the best advice is to find a potential application to a biological problem and publish the software in Bioinformatics or other similar journals. Regards, Ovidiu ====================================================================== Sent to CCL by: "TJ O'Donnell" [tjo^-^acm.org] Well, I've been staying out of this fray, but having just started to market a closed-source product, this issue has been on my mind a lot over the past year. Warren writes: > The only way to publish software in a scientifically robust manner is to > share source code, and that means publishing via the internet in an > open-access/open-source fashion. Anything short of that amounts to > issuing unproven claims based on limited empirical tests regarding what > a given program allegedly does. What is that called outside of science? > Advertising! And as such, I agree that it does not belong in a > scientific journal. Either you publish software with source code and > stand behind it, or you are blowing smoke and quite *literally* hiding > something -- no matter how noble your intent. This is a rather extreme statement, that needs to be tempered, IMHO. Hiding source code is NOT tantamount to deception, as is implied above. Results of a program are, perhaps, the only ~scientifically~ relevant aspect of a program; the only useful effect of it; and the only thing that must be subject to scientific scrutiny. Results MUST be carefully considered, reviewed and verified. If they are in error, one must consider the assumptions, theory, algorithms and, of course, the code behind those erroneous results. Do instrument designers publish their schematics (I honestly don't know). Does Varian, et. al.? Does that make those instruments tantamount to scientific fraud? Absolutely not! Why? Because the RESULTS (spectra, etc.) are subject to intense scientific scrutiny. Let me just finish by saying that I subject my own programs to intense scientific scrutiny and welcome such from my users. It becomes my responsibility to correct errors, as any experimentalist does. For those who may be interested, my new work is at: http://www.gnova.com/ Sincerely, TJ O'Donnell, Ph.D. gNova Scientific Software http://www.gnova.com/ ====================================================================== Sent to CCL by: "Warren DeLano" [warren*|*delsci.com] > From: TJ O'Donnell [mailto:tjo*acm.org] > > Warren writes: > > The only way to publish software in a scientifically robust > manner is > > to share source code, and that means publishing via the > internet in an > > open-access/open-source fashion. Anything short of that amounts to > > issuing unproven claims based on limited empirical tests regarding > > what a given program allegedly does. What is that called > outside of science? > > Advertising! And as such, I agree that it does not belong in a > > scientific journal. Either you publish software with > source code and > > stand behind it, or you are blowing smoke and quite > *literally* hiding > > something -- no matter how noble your intent. > This is a rather extreme statement, that needs to be tempered, IMHO. > Hiding source code is NOT tantamount to deception, as is > implied above. No -- let me clarify -- I do not imply that closed-source is tantamount to deception. It is simply non-disclosure -- a willful holding back of pertinent helpful information. It is tantamount to saying "trust me" -- I have correctly applied chemistry, physics, math, and computer science to create a working solution to your problem. Thorough testing of closed-source code can of course lay an empirical foundation for extending such trust, and testing is equally necessary with open-source code. But testing alone is not the same as disclosing an implementation that can itself be subjected to direct intellectual scrutiny. While there are valid personal, economic, political, legal, practical, and insitutional reasons for not disclosing source code, I challenge anyone to come up with a compelling scientific reason for why source code should not be disclosed -- when possible -- to enable understanding, reproduction, verification, and extension of computational advances. Is there ever a legitimate *purely scientific* reason for settling with empirical evidence alone (just test results) when mathematical proof is itself attainable (via inspection of source code)? I cannot think of any. Or are we all agreed that making source code available is the *scientific* ideal to which we should all aspire? If so, then when we do not make source available, we should certainly have some compelling non-scientific reason for holding it back, and as honest scientists, we must realize that doing so will have the effect of limiting the value and impact of our work -- at least from a scientific standpoint. Intellectual advances are either shared or lost, and software implementations are no exception to this. Cheers, Warren PS. A trivial concrete illustration: I write some function called "add_two_numbers" and share it will my colleagues. And for the millions of pairs of numbers they test it on, it returns the sum. So much so good. But without source, no one can even be sure that there isn't some untested pair of numbers for which it fails. Now I share the source: def add_two_numbers(a,b): return a+b > From that point on, everyone can sleep well knowing for certain that my function will always return the sum of two numbers, since the implementation is public and exact. Science can progress because Warren has re-implemented addition. Hooray! On the other hand, if the source was reveald to be: def add_two_numbers(a,b): if (a == 1823723) and (b == 8374723): return 6 else: return a+b Then everyone would immediately know for certain that my function is flawed and needs to be fixed. Could testing have found this? Assuming that the inputs are 32-bits wide, then there are 2^64 combinations of possible inputs with only one flaw. 2^64 is far too many inputs to practially examine, so this flaw would almost certainly never have been found through testing. Thus, even in the simplest function, it is possible to introduce a flaw that cannot be found through rigorous regression testing. Admittedly this example is contrived, but it isn't hard to see how testing can easily miss subtle problems that could well be identified through critical analysis of source code. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren*delsci.com ====================================================================== Sent to CCL by: Cory Pye [cpye[-]crux.smu.ca] On Fri, 14 Oct 2005, Warren DeLano warren],[delsci.com wrote: > No -- let me clarify -- I do not imply that closed-source is tantamount > to deception. It is simply non-disclosure -- a willful holding back of > pertinent helpful information. It is tantamount to saying "trust me" -- > I have correctly applied chemistry, physics, math, and computer science > to create a working solution to your problem. Every time somebody publishes a paper, there is a matter of trust inherent between the readers, journal, and author. This trust entails, for example, the author declaring "I did not fabricate my data", "I have not already published this work elsewhere", and the editor declaring "This manuscript has undergone a rigorous peer-review process", "I did not let any personal connection with the author influence my views", etc. There is a certain amount of trust inherent in scientific publishing. A (complicated) program is the author's "baby", and it is up to the author as to whether he or she wishes to make it publically available. I don't think that the trust argument is applicable here, as it is an inevitable fact. One difficulty with making a program publically available is it can mutate into a non-viable form by an inexperienced programmer, and if the mutant happens to be widely circulated, then a lot of the blame ends up on the original programmer, who has essentially given up his "baby" for adoption, instead of the modifier. One can easily waste weeks of time addressing irate "customers" because of someone else's goof-up. > > Thorough testing of closed-source code can of course lay an empirical > foundation for extending such trust, and testing is equally necessary > with open-source code. But testing alone is not the same as disclosing > an implementation that can itself be subjected to direct intellectual > scrutiny. > > While there are valid personal, economic, political, legal, practical, > and insitutional reasons for not disclosing source code, I challenge > anyone to come up with a compelling scientific reason for why source > code should not be disclosed -- when possible -- to enable > understanding, reproduction, verification, and extension of > computational advances. Suppose a junior faculty member publishes a paper and publicly releases some code with his first graduate student. The idea becomes so popular that a senior researcher or company takes that open-source code, with acknowledgements, and incorporates it into a popular commercial program, with some modifications and writes 2 or 3 papers describing the advances. Science is advanced. Lots of people use it, but only quote the paper in the manual of the senior researcher. Now suppose that the advances were supposed to be the rest of the graduate student's Ph. D. work. This student cannot re-publish this work because the other ideas have been published already by the borrower. The junior faculty, for lack of sufficient publications, loses his grant, and is denied tenure. The student's thesis, being mostly unpublishable, is not accepted. Has science advanced at the expense of the careers of the two individuals? Are computational chemists a species known for eating their young? :-) Had the junior faculty member not disclosed his source, it would have been more difficult for this hypothetical travesty to happen. The sad reality is that things like this can and do happen and a little paranoia goes a long way. It would have been far better if the company had approached the junior faculty and come to an agreement. In order to be able to do your own science, pragmatics such as having tenure, a grant, etc. have to be looked at first. It is a lot less stressful (and the temptation to cut corners less i.e. thorough testing) to implement a new code, building on some older code, when you don't have someone breathing down your neck trying to outdo you. Writing and debugging code is a lot of effort, and you want to be rewarded for your efforts, either through publications, citations, or financial remuneration. I would like to say for the record that my experience coding the COSMO routine within the ADF package (97-99) has been absolutely wonderful, as I have found SCM to be very cooperative in pointing out my errors and vice versa. I am also grateful to the many users who have been patient when they hit the occasional snag, esp. Heiko Jacobsen and Michael Atanasov. Through dialogue the resulting code was much better. I will certainly celebrate with a bottle of good scotch when I hit 100 citations on the TCA paper describing our implementation either late his year or early next year. > > Is there ever a legitimate *purely scientific* reason for settling with > empirical evidence alone (just test results) when mathematical proof is > itself attainable (via inspection of source code)? I cannot think of > any. > Source code is "not" mathematical proof, just ask anyone who had to use a buggy Fortran compiler, say when the runtime "check array bounds" debugging option, didn't work with a character array. > Or are we all agreed that making source code available is the > *scientific* ideal to which we should all aspire? > > If so, then when we do not make source available, we should certainly > have some compelling non-scientific reason for holding it back, and as > honest scientists, we must realize that doing so will have the effect of > limiting the value and impact of our work -- at least from a scientific > standpoint. Intellectual advances are either shared or lost, and > software implementations are no exception to this. > > Cheers, > Warren > > [stuff deleted] ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye .. crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) ====================================================================== Sent to CCL by: "Warren DeLano" [warren() delsci.com] Dear Cory, Thank you for that response, which includes excellent discussion of the "valid personal, economic, political, legal, practical, and insitutional reasons for not disclosing source code" to which I referred. Releasing source code can very well make it harder for the involved parties to do *more science*, due to distraction, giving up control, lack of proper credit, loss of funding, risk of tenure, and so forth. But also understand that by not releasing source code, you absolutely deny the rest of the scientific community the opportunity of doing *more science* using your source code. Perhaps your TCA paper would now have 1,000 citations had the code been open from the start. Who can say? It depends. Regardless, both sides of the above argument are pragmatic in nature and do not address the question I again pose: If we solely consider the standards of disclosure, verifiability, and reproducibility inherent in the scientific method, is it not the case that sharing source code comes much closer to meeting that ideal than does not sharing source code? And if so, then as good scientists, shouldn't we seek opportunities to advance science through open source scientific code, whenever possible, while fully taking into account pragmatic concerns like those you described? Cheers, Warren PS. Aside... > Source code is "not" mathematical proof, just ask anyone who > had to use a buggy Fortran compiler, say when the runtime > "check array bounds" debugging option, didn't work with a > character array. Source code is a symbolic representation of an information process that has a precise mathematical meaning, subject to the nature of the implementation language. One can indeed prove mathematical equivalence or non-equivalence between an abstract mathematical expression and the mathematical meaning of a given source code implementation. For example, take the expression "F=ma", and the source code implementation "def F(m,a): return m*a". In Python, this implementation is proven to be correct to the precision limits of the double-precision numeric representation. In contrast "def F(m,a): return m+a" is proven to be non-equivalent. In other words, having a broken "+" key on a calculator does not invalidate Addition any more than having a broken Fortran compiler invalidates the mathematical validity of the Fortran program you compile. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren]![delsci.com ====================================================================== Sent to CCL by: John McKelvey [jmmckel : attglobal.net] Corey Pye commented: "One difficulty with making a program publically available is it can mutate into a non-viable form by an inexperienced programmer, and if the mutant happens to be widely circulated, then a lot of the blame ends up on the original programmer, who has essentially given up his "baby" for adoption, instead of the modifier. One can easily waste weeks of time addressing irate "customers" because of someone else's goof-up." I believe that this is exactly what happened to one version of Gaussian when someone hacked a d-orbital capability and got it wrong ... John McKelvey ====================================================================== Sent to CCL by: "Perry E. Metzger" [perry*|*piermont.com] "Cory Pye" writes: > One difficulty with making a program publically available is it can > mutate into a non-viable form by an inexperienced programmer, and if > the mutant happens to be widely circulated, then a lot of the blame > ends up on the original programmer, who has essentially given up his > "baby" for adoption, instead of the modifier. One can easily waste > weeks of time addressing irate "customers" because of someone else's > goof-up. I've been writing open source software for something like 15 years now. I've never once had this happen to me or to anyone I know -- not once. > Suppose a junior faculty member publishes a paper and publicly > releases some code with his first graduate student. The idea becomes > so popular that a senior researcher or company takes that > open-source code, with acknowledgements, and incorporates it into a > popular commercial program, with some modifications and writes 2 or > 3 papers describing the advances. Science is advanced. Lots of > people use it, but only quote the paper in the manual of the senior > researcher. > > Now suppose that the advances were supposed to be the rest of the graduate > student's Ph. D. work. This student cannot re-publish this work because the > other ideas have been published already by the borrower. Well, suppose you publish some research and, even without the use of your code, other people make advancements that you wanted to make first just by looking at your work and saying "hey, this is a cool thing to try next". Tough luck for you. That's how science works. Of course, if you aren't silly, you don't mind and it doesn't hurt you. Einstein didn't come up with spacetime -- Minkowski did, looking at Einstein's 1905 papers. Did Einstein then winge "you did that before I could"? No. Did Poincare spend all his time complaining that Einstein was influenced by him and published first? No. As it happens, I've had code I've written incorporated into commercial products that have made other people money and I haven't gotten a nickel. I've had code I've written taken by others, improved and re-released as open source, too. I have no regrets at all and continue to write open source software. My goal when I release something is for it to be used, you see. If no one uses it, it's as useless as writing a symphony no one will ever hear or painting a canvas no one will ever see. Who wants that? > Has science advanced at the expense of the careers of the two individuals? I'm going to be so bold as to say that science doesn't exist to advance people's careers, and that good science isn't done very often by people so obsessed with careerism that they withhold information in the hope of gaining an edge over scientific competitors. I'll go further and say that people obsessed with their careers to this extent don't actually have good ones, either on the level of enjoying them or on the level of getting ahead. Not so paradoxically, doing good work is more important than relentless scheming and gamesmanship. That doesn't mean you should ignore personal advancement, but it does mean that spending all your time being a backbiting bitter schemer doesn't really do as much good as having good ideas and getting them out. If you want to live in a world filled with smart people who withhold information from each other and spend their whole time being cuthroats, become a hedge fund manager instead of a chemist. Most chemists are smart enough to do that for a living, and it pays literally orders of magnitude (no exaggeration) better than chemistry. If your goal is not to live in that sort of world -- if the reason you are in science is because you love science (and if you are in science for any other reason you're probably foolish -- the money sucks and the recognition sucks compared to almost anything else a smart person can do for a living), then feel happy that others have built on your work and build further on it or do something else interesting. The whole point of science is for people to stand on each other's shoulders, not on each other's feet. Long ago in my computer science career I was one of the co-inventors of a computer security protocol that is currently in use by a large fraction of the planet. (It is called "IPSEC" for those that know anything about such things.) Very quickly after I helped create it, other people became far more expert on it than I was and advanced it far past where we started. Am I bitter? Of course not. If you're bitter about stuff like that you're in the wrong field of endeavor. I'm HAPPY. The thing I helped bring into the world grew up and had a life past me. > The sad reality is that things like this can and do happen and a little > paranoia goes a long way. So you claim, but I really think you're presenting a very twisted view of the world. If you really live your life that way, you're going to be bitter all the time instead of productive. >> Is there ever a legitimate *purely scientific* reason for settling with >> empirical evidence alone (just test results) when mathematical proof is >> itself attainable (via inspection of source code)? I cannot think of >> any. > > Source code is "not" mathematical proof, No, but it is just as valuable to show your code to someone as to say what your equipment was, and IMHO just as necessary. By the way, I'll point out that the bioinformatics guys seem to be doing all of this right. They don't seem to spend all their time being paranoid that someone out there might actually USE something they built as intended -- they seem happy when it happens. They've got big public databases filled with useful information, lots of tools anyone can use, they code in high level languages, they aren't insanely secretive, etc. I think they're a good model to follow. Perry ====================================================================== Sent to CCL by: Cory Pye [cpye:_:crux.smu.ca] On Sat, 15 Oct 2005, Perry E. Metzger perry[]piermont.com wrote: > > Sent to CCL by: "Perry E. Metzger" [perry*|*piermont.com] > [stuff deleted] > > Well, suppose you publish some research and, even without the use of > your code, other people make advancements that you wanted to make > first just by looking at your work and saying "hey, this is a cool > thing to try next". Tough luck for you. That's how science works. Of > course, if you aren't silly, you don't mind and it doesn't hurt > you. Einstein didn't come up with spacetime -- Minkowski did, looking > at Einstein's 1905 papers. Did Einstein then winge "you did that > before I could"? No. Did Poincare spend all his time complaining that > Einstein was influenced by him and published first? No. > Sure, this can happen. When you publish a paper, you allow your ideas to be peer-reviewed, then adapted by others to suit their needs. If I had plans to publish a followup article, I would probably not release the source until after it was published. I am certainly not obligated to HELP others scoop my ideas by giving them my source. One shouldn't underestimate the educational benefit of having to re-implement code. Re-writing code gives you a much greater appreciation and understanding of the original author's work. In some ways, this is similar to drug companies having a 5 or 10 year patent protection from generics. Perhaps a similar thing, but shorter time (2-3 years), could be a useful compromise. In my case, the original idea was Klamt's. I took a buggy and limited implementation in ADF 2.0, reincorporated it into 2.3, then reincorporated it into ADF98 development version, which was a major rewrite because of the change in the integration details. At that point I gave the code to ADF so that they could maintain it, and wrote up the paper describing the finer details of the implementation. I encourage folks when they use ADF COSMO to cite both my paper, and the original paper of Klamt. There are numerous versions of COSMO now, as implemented in Gaussian 92 (Truong), Gaussian 98 (Barone), ADF (me), DMol, MNDO/d, PARAGAUSS, GAMESS-US, etc. The details of the implementation are described in the papers. If I had kept it totally to myself, only in ADF 2.3, it would now be obsolete. By giving it to SCM and the affiliated developers, it has a life of its own. Lots of people use it and suggest improvements, even though it isn't open source. I'm quite happy to see people using and acknowledging it, I don't want money for it. [stuff deleted] > > I'm going to be so bold as to say that science doesn't exist to > advance people's careers, and that good science isn't done very often > by people so obsessed with careerism that they withhold information in > the hope of gaining an edge over scientific competitors. I'll go > further and say that people obsessed with their careers to this extent > don't actually have good ones, either on the level of enjoying them or > on the level of getting ahead. Not so paradoxically, doing good work > is more important than relentless scheming and gamesmanship. That > doesn't mean you should ignore personal advancement, but it does mean > that spending all your time being a backbiting bitter schemer doesn't > really do as much good as having good ideas and getting them out. This is true. However, if the hypothetical professor in my previous e-mail doesn't get tenure and his student doesn't get his Ph. D., then the short-term advancement in science is more than nullified by the fact that these two individuals now cannot make any further contributions in academia. Who would re-hire a person denied tenure or without a Ph. D.? They are consigned to a sessional appointment or lecturer position with no possibility of advancement. I feel that the long-term scientific contributions are traded for short-term gain. [stuff deleted] > > The sad reality is that things like this can and do happen and a little > > paranoia goes a long way. > > So you claim, but I really think you're presenting a very twisted view > of the world. If you really live your life that way, you're going to > be bitter all the time instead of productive. I know of people who go to conferences to hear talks about unpublished work by some junior guy or person at a small institution, essentially stealing their ideas, then put their army of 20 postdocs on the same problem in an attempt to beat them to the press. I have also heard of senior faculty rejecting grant proposals from junior guys, and submitting a very similar proposal in the next round. If push comes to shove, who will be believed, the senior or junior guy? Perhaps one's paranoia can be switched off once one has the letter from the university president congratulating you on one's tenure and promotion to associate :-) I propose a new reality TV show called "Tenure-Track". It would be a cross between "Survivor" and "Cops". [more stuff deleted] ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye%a%crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) ====================================================================== Sent to CCL by: Steve Bowlus [chezbowlus_+_goldrush.com] $0.02 from a (grateful) enduser (who can't spell "C") of everyone else's code: At one time, the CompChem community had its own vehicle for this purpose. It was (and still is) called the "Quantum Chemistry Program Exchange." For nominal cost (basically then media costs), academics and industry could get access to cutting edge programming. As QCPE matured in the mid- to late '80's, there was published (again, at modest cost) the quarterly "QCPE Bulletin," in which contributors could (as my memory serves me) publish exactly the kind of information being debated in this thread. Descriptions of new contributions were made in every issue by the director/editor (Richard Counts/Peggy Edwards). A uniform mechanism was provided for citation of contributions. I would suggest it is time to re-examine the utility of such a repository, and revive it along the lines envisioned by Counts. I don't know how IU currently supports QCPE (AFAIK, its capabilities are considerably curtailed); Jan's experience in obtaining funding for CCL does not bode well for the venture. But perhaps someone knowledgeable in these areas might inquire. Cheers, Steve ====================================================================== Sent to CCL by: "Noel O'Boyle" [no228{}cam.ac.uk] On Mon, 2005-10-17 at 06:57 -0700, Steve Bowlus chezbowlus[*]goldrush.com wrote: > Sent to CCL by: Steve Bowlus [chezbowlus_+_goldrush.com] > $0.02 from a (grateful) enduser (who can't spell "C") of everyone else's > code: > > At one time, the CompChem community had its own vehicle for this > purpose. It was (and still is) called the "Quantum Chemistry Program > Exchange." For nominal cost (basically then media costs), academics and > industry could get access to cutting edge programming. Things have improved in this regard since the 80s. The facilities provided by open-source repositories such as SourceForge (http://www.sf.net) are light-years beyond simple dump-it-and-leave-it-there type repositories. For example, SourceForge provides, for each program, a web site, a CVS repository (this is for coordinated the work of several developers), mailing lists, forums, bug trackers and feature requests. Whether one uses these or not is up to the individual developer(s). And it's cheaper than the QCPE - it's free for users *and* developers! > As QCPE matured > in the mid- to late '80's, there was published (again, at modest cost) > the quarterly "QCPE Bulletin," in which contributors could (as my memory > serves me) publish exactly the kind of information being debated in this > thread. Descriptions of new contributions were made in every issue by > the director/editor (Richard Counts/Peggy Edwards). A uniform mechanism > was provided for citation of contributions. Anything that provides a mechanism for developers to tell users about their software, as well as providing an encouragement for people to share code openly, sounds good to me. I would prefer though a more formal publication procedure with a peer review process, examples of which have been mentioned in both Physics and Bioinformatics. Dropping the Q in QCPE might also be a good idea; and it would encourage people to share code in the wider chemistry community. Regards, Noel ====================================================================== Emails that did not appear on the list: ====================================================================== Dear Noel, Computer Physics Communications (published by Elsevier). We published a code there recently. Best regards, Per-Olof Åstrand ====================================================================== Hi Noel, Publishing an article concerning software could be difficult. However, an article describing the application of a program to solve particular chemical problem (compounds, reactions, mechanism, etc.) is much easier to publish. So, find an application for your programs and show on the example how it works. Solve some chemically important problem using G03 and your program. The results can be easily published and you may include the description of key-features of your program in this publication. Best regards, Valentin. Zelinsky Institute of Organic Chemistry, Moscow. ====================================================================== Dr Noel O'Boyle: I saw you message in the CCL list. If your programs are related with biological research, then please take a look at www.bioinformation.net. Its an open source forum for bioinformatics and related work. We shall be happy to consider your manuscript describing the programs if they have biological applications. Sincerely, Sandeep Kumar Member, Editorial Board, Bioinformation.net ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, ====================================================================== On Oct 11, 2005, at 10:45, Noel O Boyle no228 ~~ cam.ac.uk wrote: > Where can one publish articles on programs that are of general interest > to computational chemists, but which do not contain new algorithms? There's a list of places to publish comp chem at http://membership.acs.org/C/COMP/resources.html#Anchor-Publishing-47857 , perhaps some of them might be appropriate. Lisa -- ------------------------------------------------------------------------------------------------------------------------------- Lisa M. Balbes, Ph.D. lisa],[balbes.com http://www.balbes.com/ Balbes Consultants Scientific Writing/Editing since 1992 American Chemical Society - St Louis Section Treasurer, COMP division WebMaven ACS/Career Services Presenter and Career Consultant Chair, Washington University APAP, St Louis South Committee Consultants and Independent Contractors SIG Manager, St Louis Society for Technical Communication Advancement Coordinator, Boy Scout Troop 352 ====================================================================== Hello Noel! A good place for this is Computer Physics Communications, published by Elsevier. kind regards, Scotty http://www.chem.ubc.ca/personnel/faculty/scotty/index.shtml ====================================================================== > In addition, science should involve building on someone else's > work, not > reinventing the wheel. Wouldn't it be better if authors made their > code > available so that others could use it? Yes! And of course that's the point of open source. :-) It make sense in the context of science, where building on old work and peer review is expected. I was just asked to give a talk on Open Babel at a nanoscience workshop, so maybe things are changing. Everyone seemed happy about the ideas of programs like GaussSum and Open Babel. I hope you find a place to publish an article -- people seem to be unhappy about citing programs that don't have publications. Except Gaussian itself... I guess that's OK to cite even though it's not published anywhere. Cheers and best regards, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruña Group http://abruna.chem.cornell.edu/ ====================================================================== Hi Noel, Let's consider MOLDEN as example. I always cite the reference suggested by the author of MOLDEN, when I use this program. Even if that reference does not provide all the information about the particular MOLDEN option, still it is very useful to cite it. The readers may find general information about the program features and the link to website, where complete manual is given. So, if you suggest a reference (a few references) for the users of your software, most likely these references will be cited. Writing software seems very easy from the users' point of view (those who never did it) and it is really hard task from the other side. You should be able to use some benefits in terms of citation associated with your program. As you can see from the CCL replies most of the community is against publishing articles about programs. One of the editors told me: "we don't publish software manuals, we publish chemistry." Best regards, Valentin. > Dear Valentin, > Thanks for your answer. > > I'm familiar with this method of publication, and it's true that I've > used my program to do some science. However, it's not really a valid way > of spreading information about the program's features. For example, it > does not make a lot of sense to reference a paper about ruthenium > chemistry (in my case) just because you used my software. Also, the > reviewers will rightly say that a long description of features of > gausssum is not appropriate to the topic of the paper. > > If I cannot find any other way to do it, I will follow your advice, but > I regard it as a workaround for the current situation in chemistry, > rather than the ideal solution. > > Thanks again, > > Noel ====================================================================== From owner-chemistry@ccl.net Tue Oct 25 07:17:00 2005 From: "Vlad Cojocaru Vlad.Cojocaru---eml-r.villa-bosch.de" To: CCL Subject: CCL: Gamess problem: error message missing Message-Id: <-29723-051025064316-26200-D93sDSvgnmaRqVcRXGbfVA(_)server.ccl.net> X-Original-From: Vlad Cojocaru Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 25 Oct 2005 12:42:50 +0200 MIME-Version: 1.0 Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru^eml-r.villa-bosch.de] Dear CCL ers, Please except my appologies .. In my previous email about the gamess program I forgot to give you the error message that I get. Here is the error message that I get when trying to run gamess on single CPU under Debian Linux: "Running gamess.Jun202002R1.x on localhost as compute process 0 ** Address Error ** ddikick: Trapped SIGCHLD: Unexpected termination of a child process." Of course the gamess.Jun202002R1.x is my executable Sorry for the missing info!! Cheers vlad -- Dr. Vlad Cojocaru EML Research gGmbH Molecular and Cellular Modeling Group Villa Bosch Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Germany Phone: +49-6221-533266 Fax: +49-6221-533298 e-mail: Vlad.Cojocaru||eml-r.villa-bosch.de From owner-chemistry@ccl.net Tue Oct 25 09:04:06 2005 From: "kevin abbot kevanabbot*yahoo.com" To: CCL Subject: CCL: W:bounded DNA-Protein Docking Message-Id: <-29725-051025070427-7797-WZYrvqLc5brsdTDiFc9JTA#server.ccl.net> X-Original-From: "kevin abbot" Sent to CCL by: "kevin abbot" [kevanabbot]^[yahoo.com] Hi all, I'm interested in docking DNA into a protein with a covalent bond among these two biopolymers. Is there some programs (possible free) that do this kind of docking? regards kevin From owner-chemistry@ccl.net Tue Oct 25 08:30:03 2005 From: "Olegas Eicher-Lorka lorka[-]ktl.mii.lt" To: CCL Subject: CCL: bigger single-core or smaller dual-core? Message-Id: <-29724-051025080349-29365-Ph8lMWaIPUMF4XZgN1PYMA]|[server.ccl.net> X-Original-From: "Olegas Eicher-Lorka" Content-Type: multipart/alternative; boundary="----=_NextPart_000_00E5_01C5D96F.05621B40" Date: Tue, 25 Oct 2005 14:18:50 +0300 MIME-Version: 1.0 Sent to CCL by: "Olegas Eicher-Lorka" [lorka(_)ktl.mii.lt] This is a multi-part message in MIME format. ------=_NextPart_000_00E5_01C5D96F.05621B40 Content-Type: text/plain; charset="windows-1257" Content-Transfer-Encoding: quoted-printable Dear all: Which is the better performance/price choice for computational chemistry = (energy and frequency jobs) : Two dual-core AMD Opteron 1.8GHz(265) or four single-core AMD Opteron = 2.4GHz(250) ? Thanks to all: Olegas ------=_NextPart_000_00E5_01C5D96F.05621B40 Content-Type: text/html; charset="windows-1257" Content-Transfer-Encoding: quoted-printable
 
Dear all:
Which is the better performance/price choice for computational = chemistry=20 (energy and frequency jobs) :
Two dual-core AMD Opteron 1.8GHz(265) or four single-core AMD = Opteron=20 2.4GHz(250) ?
 
Thanks to all:

Olegas
------=_NextPart_000_00E5_01C5D96F.05621B40-- From owner-chemistry@ccl.net Tue Oct 25 09:39:01 2005 From: "Laurynas Riauba laurynas.Riauba]_[chf.vu.lt" To: CCL Subject: CCL: Vibrational analysis Message-Id: <-29726-051025090152-12082-+Ba3Dkx1C8WC5jJIHlha7w^server.ccl.net> X-Original-From: Laurynas Riauba Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 25 Oct 2005 15:05:30 +0300 MIME-Version: 1.0 Sent to CCL by: Laurynas Riauba [laurynas.Riauba!=!chf.vu.lt] Dear CCLers, I'm doing vibrational analysis with some organic molecules and I have got some strange results. Calculations were performed with Gaussian 03 and calculated vibrational frequencies in output file are in quite good agreement with experimental data. But when I try to calculate these frequencies using only cartesian force constants and cartesian coordinates, I get very different results. Below are listed main steps of calculation: 0. Assume, that molecule has C1 symetry, has N atoms, 3N-6 vibrations 1. Converting *.chk to *.fch 2. Extraction of cartesian force constants from *.fch and converting extracted data to a matrix of size 3N * 3N (*.fch lists only triangular matrix elements). Denote this matrix FX 3. Extraction of cartesian coordinates of atoms from *.fch and scaling extracted data with a value of 0.529177237. 4. Creation of B matrix. This step was done with BMat program from QCPE, and input for that program i have used properly formated file with cartesian coordinates from step3 and 3N-6 internal coordinates(indeed these coordinates were generated using Prometheus program for windows). Output from BMat program was formated to give B matrix of size (3N-6)*(3N), where 3N is number of columns 5. Creation of diagonal M matrix with size 3N*3N and filled with atomic weight values 6. Calculation of G matrix: G = B * M(-1) * B' 7. Calculation of force matrix F in internal coordinates representation: F = B * FX * B' 8. Calculation of GF matrix: GF = G*F 9. Calculations of GF eigenvalues and eigenvectors. 10. It is stated, that eigenvalues of GF matrix (denote Lambda) are connected with vibrational frequence Liambda(k) = 4 * sqr(PI) * sqr(v(k)), where Liambda(k) is k-th eigenvalue and v(k) is frequency of vibration. Frequency can be converted to wavenumbers by dividing it with c, speed of light. And the last thing, units have to be converted. After all these calculations I get frequencies, which are totally different compared to frequencies from gaussian output. Is this calculation scheme correct? Thank you in advance Laurynas Riauba PhD student, Faculty of Chemistry Vilnius University, Vilnius, Lithuania From owner-chemistry@ccl.net Tue Oct 25 10:14:00 2005 From: "Ding Xunlei dxl#ustc.edu.cn" To: CCL Subject: CCL: calculation on C60 using DMol3 Message-Id: <-29727-051025091732-16144-5ntI5CsinuADGjqzj/Ti/Q|-|server.ccl.net> X-Original-From: "Ding Xunlei" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Tue, 25 Oct 2005 21:17:21 +0800 Mime-Version: 1.0 Sent to CCL by: "Ding Xunlei" [dxl%ustc.edu.cn] Dear All£º I used 1.45327 and 1.36701 (angstrom) for single and double bonds in C60, the calculation will have a error. ¡¡¡¡I now find that using the bond lengths 1.452 and 1.399 for single and double bonds in C60, the calculation is successful. I don't know why. Thank you for your help! Yours sincerely, Ding Xunlei 2005-10-25 ______________________________________________ ======= 2005-10-25 11:31:02 You have written: ======= > >Sent to CCL by: "Ding Xunlei" [dxl%%ustc.edu.cn] >Dear CCLs, > >I get an error when I do an energy calculation on C60 with DMol3, using dnd basis set and set "symmetry on"( C60 has Ih symmetry). The message is below: >"Point group symmetry ih symmetry orbital prototypes generated (SYMDEC) >Too many coefficients procof **** in T1U.1 >Message: DMol3 job failed >Error: DMol3 exiting" >If set "symmetry off" or use dn basis set, the calculation is successful. >Then how can I do the calculation with symmetry on and dnd basis set? > >Thank you! > > >Yours sincerely, >Ding Xunlei >2005-10-25 >______________________________________________> > > >. = = = = = = = = = = = = = = = = = = = = From owner-chemistry@ccl.net Tue Oct 25 10:49:01 2005 From: "Jane Ou janeou.:.che.rochester.edu" To: CCL Subject: CCL: W:Transition Dipole Moments with Gaussain 03 Message-Id: <-29728-051025101116-24628-VRt7CYWKD936Sa29ycPsjA\a/server.ccl.net> X-Original-From: "Jane Ou" Sent to CCL by: "Jane Ou" [janeou=-=che.rochester.edu] Dear Sirs: What is the general accuracy of the computed transition dipole moments using Gaussian 03 with TD B3LYP/6-31G(d) functionals? Are there any data or literatures I can look into? Thank you. Sincerely, Jane From owner-chemistry@ccl.net Tue Oct 25 11:24:00 2005 From: "Istvan Mayer mayer-#-chemres.hu" To: CCL Subject: CCL: W:Bond order and virial-theorem based energy decomposition program Message-Id: <-29729-051025110822-28192-TL7fmqAOlz/iGNJ0A+nVDw ~ server.ccl.net> X-Original-From: "Istvan Mayer" Sent to CCL by: "Istvan Mayer" [mayer-,-chemres.hu] Dear CCL-ers, this is to inform you that a new small program called BO-VIR has been prepared for calculating BOND ORDER and VALENCE INDICES, as defined in I. Mayer, Chem. Phys. Lett. 97, 270, 1983 (closed shell), ibid. 117, 396, 1985 (open shell) etc. as well as ENERGY DECOMPOSITION based on the VIRIAL THEOREM. It can be used at the RHF, UHF level, and is applicable to large systems, too. The program uses my original bond order routine of 1982/83 and some routines from the program APOST by I. Mayer and A. Hamza (Budapest, 2000) The program requires only a formatted checkpoint file calculated in a Gaussian run (G92...G03). It is applicable for large systems (up to 2000 orbitals) and can easily be extended further. The program may be freely downloaded from our website http://occam.chemres.hu where other programs of our group (other energy decomposition, fuzzy atom analysis, prediction of primary mass spectrometric fragmentations etc.) are available, too. Istvan Mayer ------------------------------------------------------ Prof. Istvan Mayer Chemical Research Center Hungarian Academy of Sciences H-1525 Budapest, P.O.Box 17, Hungary Phone: (+361) 438-4141, 438-4123 (ext.295,107) Fax: (+361) 325-7554, 325-7750 e-mail: mayer*at*chemres.hu ------------------------------------------------------ From owner-chemistry@ccl.net Tue Oct 25 11:59:00 2005 From: "Richard Wood rwoodphd%msn.com" To: CCL Subject: CCL: help needed Message-Id: <-29730-051025102656-6277-5MUfiH69YKE+0hQ91eyKPQ_._server.ccl.net> X-Original-From: "Richard Wood" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=response Date: Tue, 25 Oct 2005 10:26:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Richard Wood" [rwoodphd[A]msn.com] Hi all, Thanks to those whom have offered suggestions so far. Last night I discovered a problem that I don't think is related to the large velocities encountered when I begin an MD simulation in NAMD. The protein that I was trying to do calculations on has two chains, A and B. There are about 350 residues in each chain or do, and each is numbered consecutively in each chain. That is, they are numbered 1, 2, 3 ... in Chain A, and 1, 2, 3 ... in Chain B as well. Thus, when I run them through my script in psfgen, I lose the B chain residues! So when I look at the molecule, I have half the protein, but the waters surround the B chain are there. I guess the residues of Chain B need to be renumbered, but I don't know of an "easy" way to do this, other than to do a "Replace" in a word processor. As I said, this is a new problem, unrelated to the others, but one I am sure will occur again and again. Thank you for your help, Richard Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 rwoodphd(_)yahoo.com ----- Original Message ----- > From: "Richard Wood rwoodphd+*+msn.com" To: "Wood, Richard L. " Sent: Monday, October 24, 2005 10:29 AM Subject: CCL: help needed > > Sent to CCL by: "Richard Wood" [rwoodphd]|[msn.com] > Hi all, > > I have some questions, some may be simple and some may not be. So, please > bear with me :) > > The first is this. Where can I find a free program that runs under > Windows that will read in a pdb file and do an energy minimization so that > I can run dynamics calculations. The pdb files have been "generated" > using psfgen that comes with NAMD. > > The second question may not be so simple. How can I generate > "Charmm-like" topologies and parameters for small molecules? Again, I > wish to use NAMD to perform dynamics calculations on these small > molecules. > > The third one may be the most difficult. I have a protein-ligand complex > that I wish to do dynamics on. The hard part is that the ligand is also a > peptide. How can I set up my peptide/system so that when I generate a psf > file and pdb from psfgen, it doesn't think that the peptide is part of the > larger protein? > > Again, any programs to do this need to be free as I am doing this all > freelance. > > Thanks in advance, > Richard > > > Richard L. Wood, Ph. D. > Computational Chemist > Cockeysville, MD 21030 > rwoodphd(~)yahoo.comhttp://www.ccl.net/chemistry/sub_unsub.shtml> > > > From owner-chemistry@ccl.net Tue Oct 25 12:34:00 2005 From: "Jane-Jane Ou janeou * che.rochester.edu" To: CCL Subject: CCL: Transition Dipole Moment with Gaussian Message-Id: <-29731-051025105607-21764-+lGU/EsVZYGzPkayKqg/Ow%a%server.ccl.net> X-Original-From: Jane-Jane Ou Date: Tue, 25 Oct 2005 10:05:19 -0400 (EDT) Sent to CCL by: Jane-Jane Ou [janeou(~)che.rochester.edu] Dear Sirs: What is the general accuracy of the computed transition dipole moments using Gaussian 03 with TD B3LYP/6-31G(d) functionals? Are there any data or literatures I can look into? Thank you. Sincerely, Jane ./ From owner-chemistry@ccl.net Tue Oct 25 13:37:01 2005 From: "Mima Staikova mima.staikova _ gmail.com" To: CCL Subject: CCL: rigid scan in Gaussian Message-Id: <-29732-051025132302-7266-WzPAl+q2ObipMAJqZsUfWA**server.ccl.net> X-Original-From: Mima Staikova Content-Type: multipart/alternative; boundary="----=_Part_15614_16162762.1130257036109" Date: Tue, 25 Oct 2005 12:17:16 -0400 MIME-Version: 1.0 Sent to CCL by: Mima Staikova [mima.staikova!A!gmail.com] ------=_Part_15614_16162762.1130257036109 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi everyone, I need to model a reaction path of hydrogen abstraction, mediated by water molecule. A hydrogen from the substrate is transferred to the water molecule and simultaneously one of the water hydrogens is transferred to the acceptor. I am interested in the energy along this pathway without reoptimizing the substrate and the acceptor at every step along the reaction coordinate. The reaction coordinate is a straight line. The Scan keyword (rigid scan) is going to give me a potential surface, not = a potential curve, if I specify the coordinates of the two hydrogens, that ar= e moving simultaneously, calculating at every coordinate change of the first = H the all the changes for the second H. How can I do the calculation in such a way that I have for each change in the first H distance to the substrate just one change in the distance for the second hydrogen, without having to resort to multiple single point calculations? Thank you. Mima Staikova ------=_Part_15614_16162762.1130257036109 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi everyone,

I need to model a reaction path of hydrogen abstraction= , mediated by water molecule.
A hydrogen from  the substrate is tra= nsferred to the  water molecule and simultaneously one of the water h= ydrogens is transferred to the acceptor. I am interested in the energy alon= g this pathway without reoptimizing the substrate and the acceptor at every= step along the reaction coordinate. The reaction coordinate is a straight = line.

The Scan keyword (rigid scan) is going to give me a potential surfa= ce, not a potential curve, if I specify the coordinates of the two hydrogen= s, that are moving simultaneously, calculating at every coordinate change o= f the first H the all the changes for the second H.

How can I do the calculation in such a way that I have for each cha= nge in the first H distance to the substrate just one change in the distanc= e for the second hydrogen, without having to resort to multiple single poin= t calculations?

Thank you.
Mima Staikova



------=_Part_15614_16162762.1130257036109-- From owner-chemistry@ccl.net Tue Oct 25 14:14:01 2005 From: "Loan Huynh huynhkl2000(a)yahoo.ca" To: CCL Subject: CCL: W:bounded DNA-Protein Docking Message-Id: <-29733-051025140439-18099-nZVztnYoa0p2u+YAOYFeTg()server.ccl.net> X-Original-From: Loan Huynh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-910503302-1130259871=:86230" Date: Tue, 25 Oct 2005 13:04:31 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000[-]yahoo.ca] --0-910503302-1130259871=:86230 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Kevin, You may want to use Autodock. It's free but you need to sign a form in order to have it for free. I have the web site below. http://www.scripps.edu/mb/olson/doc/autodock/ "kevin abbot kevanabbot*yahoo.com" wrote: Sent to CCL by: "kevin abbot" [kevanabbot]^[yahoo.com] Hi all, I'm interested in docking DNA into a protein with a covalent bond among these two biopolymers. Is there some programs (possible free) that do this kind of docking? regards kevinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtLoan Huynh M.S. Polymer and Materials Chemistry University of Toronto Work: 416-946-0040 or: 416-946-8469 Cell: 416-779-7173 *************************************************** --------------------------------- Find your next car at Yahoo! Canada Autos --0-910503302-1130259871=:86230 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi Kevin,
 
You may want to use Autodock.  It's free but you need to sign a form in order to have it for free.  I have the web site below.
 
http://www.scripps.edu/mb/olson/doc/autodock/

"kevin abbot kevanabbot*yahoo.com" <owner-chemistry_-_ccl.net> wrote:

Sent to CCL by: "kevin abbot" [kevanabbot]^[yahoo.com]
Hi all,
I'm interested in docking DNA into a protein with a covalent bond among these two biopolymers. Is there some programs (possible free) that do this kind of docking?

regards

kevin


http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml
http://www.ccl.net/spammers.txt





Loan Huynh
M.S. Polymer and Materials Chemistry
University of Toronto
Work: 416-946-0040 or: 416-946-8469
Cell: 416-779-7173
***************************************************

Find your next car at Yahoo! Canada Autos --0-910503302-1130259871=:86230-- From owner-chemistry@ccl.net Tue Oct 25 16:12:00 2005 From: "Pierre Mignon pmignon||vub.ac.be" To: CCL Subject: CCL: electronic embedding in ONIOM Message-Id: <-29734-051025152617-31696-9olITfLdW3zKA+Y29fZX5w(_)server.ccl.net> X-Original-From: Pierre Mignon Date: Tue, 25 Oct 2005 20:32:39 +0200 (CEST) Sent to CCL by: Pierre Mignon [pmignon;;vub.ac.be] Dear, Is it possible to perform electronic embedding with an ONIOM(B3LYP/6-31G*:MNDO) calculation ? I read in the manual that it is possible for ONIOM(MO:MM) calculations, but for ONIOM(QM/QM) ? Thank you in advance, Pierre. Mignon Pierre PhD Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 33 15 Fax + 32 2 629 33 17 e-mail pmignon]-[vub.ac.be From owner-chemistry@ccl.net Tue Oct 25 16:57:01 2005 From: "Robert Brunner rbrunner[-]uiuc.edu" To: CCL Subject: CCL: help needed Message-Id: <-29735-051025165251-23928-zd9//CDZHavFyOT2thLfjA(!)server.ccl.net> X-Original-From: Robert Brunner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 25 Oct 2005 14:59:12 -0500 Mime-Version: 1.0 (Apple Message framework v734) Sent to CCL by: Robert Brunner [rbrunner!A!uiuc.edu] Hello Richard, This sounds like something you should be able to do with NAMD and VMD, but I'm not all that knowledgeable about setting up simulations. However, I would recommend that you try posting your question to the namd-l mailing list: Robert On Oct 24, 2005, at 9:29 AM, Richard Wood rwoodphd+*+msn.com wrote: > > Sent to CCL by: "Richard Wood" [rwoodphd]|[msn.com] > Hi all, > > I have some questions, some may be simple and some may not be. So, > please bear with me :) > > The first is this. Where can I find a free program that runs under > Windows that will read in a pdb file and do an energy minimization > so that I can run dynamics calculations. The pdb files have been > "generated" using psfgen that comes with NAMD. > > The second question may not be so simple. How can I generate > "Charmm-like" topologies and parameters for small molecules? > Again, I wish to use NAMD to perform dynamics calculations on these > small molecules. > > The third one may be the most difficult. I have a protein-ligand > complex that I wish to do dynamics on. The hard part is that the > ligand is also a peptide. How can I set up my peptide/system so > that when I generate a psf file and pdb from psfgen, it doesn't > think that the peptide is part of the larger protein? > > Again, any programs to do this need to be free as I am doing this > all freelance. > > Thanks in advance, > Richard > > > Richard L. Wood, Ph. D. > Computational Chemist > Cockeysville, MD 21030 > rwoodphd(~)yahoo.com > From owner-chemistry@ccl.net Tue Oct 25 17:31:01 2005 From: "Perry E. Metzger perry^piermont.com" To: CCL Subject: CCL: help needed Message-Id: <-29736-051025170128-28325-eswlZp+ibq/Bsw4umt0DaA]-[server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Tue, 25 Oct 2005 17:01:17 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry-#-piermont.com] "Dr Seth Olsen s.olsen1(_)uq.edu.au" writes: > You may find your options are greater if you use something like Cygwin > under windows. I couldn't get that technical about the description, but > Cygwin essentially gives you a linux-imitating environment that runs > under windows. It is a reasonable emulation environment, though you have to recompile anything you need to use, and the edges are a bit sharp. I use it when I'm forced to set stuff up in Windows environments -- it is a lot more productive than the usual Microsoft tools. Microsoft also has a similar offering that they give away called (inexplicably) "Services for Unix". I've heard they're getting rid of it though. Performance under Cygwin will not rival performance on a real Linux box -- Windows has architectural issues that make it perform pretty badly in general, and Cygwin is just a POSIX scrim over Windows. > Cygwin is free. I think the site is www.cygwin.org or somesuch. http://www.cygwin.com/ actually. Perry From owner-chemistry@ccl.net Tue Oct 25 18:09:00 2005 From: "Arindam Ganguly arindamganguly^gmail.com" To: CCL Subject: CCL: W:Calculation of Point Group Message-Id: <-29737-051025170748-3654-31K2VQzWKWecpn069QkwwA|-|server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary="----=_Part_2169_27492544.1130264186570" Date: Tue, 25 Oct 2005 13:16:26 -0500 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly-.-gmail.com] ------=_Part_2169_27492544.1130264186570 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Huub, i am not doing either of them. the Bloodshed Dev C++ IDE has compile and ru= n commmand in it. so i am compile the C source code and executing it. it just gives me a black box. just like what we get in windows command prompt, except the fact that in windows commad prompt it mentions the path, but her= e nothing that sort of comes up. that's why i was confused as to where is the mistake. i hope this helps, thanks, Arindam On 10/25/05, Van Dam, HJJ (Huub) h.j.j.vandam|*|dl.ac.uk < owner-chemistry=-=ccl.net> wrote: > > > Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam=3D=3D=3Ddl.ac.uk] > Hi, > > Are you running this from the windows command prompt or are you double > clicking it? > > Huub > > -----Original Message----- > > From: owner-chemistry#,#ccl.net [mailto:owner-chemistry#,#ccl.net] > Sent: 24 October 2005 19:34 > To: Vandam, Huub > Subject: CCL: W:Calculation of Point Group > > Hi Serguei, > i went to the mentioned website and downloaded the symmetry.c file. i am > using Bloodshed Dev C++ IDE, it can handle C files too. i build the file > and execute but all it does is give a black command prompt box, just > like we the one we get in WinXp. i don;t understand the mistake i am > committing. > further i thought probably the zip files would be the updated version > but same thing happened. could you plz tell what is mistake i am making. > thanks=3D > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_2169_27492544.1130264186570 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Huub,
i am not doing either of them. the Bloodshed Dev C++ IDE has compile and run commmand in it. so i am compile the C source code and executing it. it just gives me a black box. just like what we get in windows command prompt, except the fact that in windows commad prompt it mentions the path, but here nothing that sort of comes up. that's why i was confused as to where is the mistake. i hope this helps, thanks,

Arindam

On 10/25/05, Van Dam, HJJ (Huub) h.j.j.vandam|*|dl.ac.uk <owner-chemistry=-=ccl.net> wrote:<= /span>

Sent to CCL b= y: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam=3D=3D=3Ddl.ac.uk]
Hi,=

Are you running this from the windows command prompt or are you double
c= licking it?

Huub

-----Original Message-----
> From: own= er-chemistry#,#ccl.net [mailto:owner-ch= emistry# ,#ccl.net]
Sent: 24 October 2005 19:34
To: Vandam, Huub
Subjec= t: CCL: W:Calculation of Point Group

Hi Serguei,
i went to the me= ntioned website and downloaded the symmetry.c file. i am
using Bloodshed= Dev C++ IDE, it can handle C files too. i build the file
and execute but all it does is give a black command prompt box, justlike we the one we get in WinXp. i don;t understand the mistake i am
co= mmitting.
further i thought probably the zip files would be the updated = version
but same thing happened. could you plz tell what is mistake i am making= .
thanks=3D



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------=_Part_2169_27492544.1130264186570-- From owner-chemistry@ccl.net Tue Oct 25 19:06:00 2005 From: "Alexander Martins Silva alex.msilva,uol.com.br" To: CCL Subject: CCL: Gaussian parallel Message-Id: <-29738-051025190350-31902-MbSl4M0Hmk2j8LN4H+jwIQ**server.ccl.net> X-Original-From: Alexander Martins Silva Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 25 Oct 2005 21:04:12 +0000 MIME-Version: 1.0 Sent to CCL by: Alexander Martins Silva [alex.msilva]=[uol.com.br] Alexander Martins Silva wrote: > > Hi, > > I was trying to execute a parallel job with Gaussian. The job > starts but not run at the nodes. > > After g03l inputefile: > > $ g03l 453.inp & > setenv GAUSS_EXEDIR > /usr/local/g03/linda-exe:/usr/local/g03/bsd:/usr/local/g03/private:/usr/local/g03 > > g03 453.inp > [2] 18731 > $ ntsnet: using global map file > "/usr/local/g03/linda7.1/intel-linux2.4-rh8/../common/lib/tsnet.map" > ntsnet: couldn't find user map file "/home/alex/.tsnet.map" > ntsnet: checking for /usr/local/g03/linda-exe/l302.exel > ntsnet: using executable file /usr/local/g03/linda-exe/l302.exel > ntsnet: maxlicense is 1000000 > ******************************************** > appl config file: /usr/local/g03/linda-exe/tsnet.config-l302_exel > user config file: /home/alex/.tsnet.config > global config file: > /usr/local/g03/linda7.1/intel-linux2.4-rh8/../common/lib/tsnet.config > user map file: /home/alex/.tsnet.map > global map file: > /usr/local/g03/linda7.1/intel-linux2.4-rh8/../common/lib/tsnet.map > local node: at1 > remote nodes: at1101 at1102 at1103 at1104 > nodelist: at1101 at1102 at1103 at1104 > nodefile: tsnet.nodes > minwait: 600 > maxwait: 600 > workerwait: 900 > masterload: 1.000000 > workerload: 1.000000 > fallbackload: 0.990000 > maxprocspernode: 1 > delay: 0 > maxnodes: Number of available nodes > minworkers: 3 > maxworkers: 3 > loadperiod: 5 > high: True > suffix: True > verbose: True > veryverbose: True > distribute: False > cleanup: True > getload: False > translate: True > useglobalconfig: True > useglobalmap: True > application name: l302.exel > application lookup name: l302_exel > local executable directory: /usr/local/g03/linda-exe > distribution directory: /usr/local/g03/linda7.1/intel-linux2.4-rh8/ > maxlicense: 1000000 > ******************************************** > ntsnet: trying to schedule 3 workers > ntsnet: scheduled a total of 3 workers > ******************************************** > node name: xxx > (...) > node name.... > (...) > ntsnet: starting master process on at1 > /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_sh > /usr/local/g03/linda-exe/l302.exel 65536000 /home/alex/Gau-18733.chk 0 > /home/alex/Gau-18733.int 0 /home/alex/Gau-18733.rwf 0 > /home/alex/Gau-18733.d2e 0 /home/alex/Gau-18733.scr 0 > /home/alex/Gau-18732.inp 0 junk.out 0 +LARGS 5 0 -kainterval 1 -master > 30997 -tsnetport 42530 -maxworkers 3 -minworkers 3 -minwait 600 > -maxwait 600 -nodename at1 -kaon > ntsnet: starting 1 worker on at1101.ime.eb.br > /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_rsh > at1101.ime.eb.br -r ssh /usr/local/g03/linda-exe/l302.exel 65536000 > /home/alex/Gau-18733.chk 0 /home/alex/Gau-18733.int 0 > /home/alex/Gau-18733.rwf 0 /home/alex/Gau-18733.d2e 0 > /home/alex/Gau-18733.scr 0 /home/alex/Gau-18732.inp 0 junk.out 0 > +LARGS 5 1 -maxworkers 3 -chdir /home/alex -worker at1:30997 > -workerwait 900 -tsnetref 1 -nodename at1101xxx > ntsnet: starting 1 worker on at1102.ime.eb.br > /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_rsh > at1102.ime.eb.br -r ssh /usr/local/g03/linda-exe/l302.exel 65536000 > /home/alex/Gau-18733.chk 0 /home/alex/Gau-18733.int 0 > /home/alex/Gau-18733.rwf 0 /home/alex/Gau-18733.d2e 0 > /home/alex/Gau-18733.scr 0 /home/alex/Gau-18732.inp 0 junk.out 0 > +LARGS 5 2 -maxworkers 3 -chdir /home/alex -worker at1:30997 > -workerwait 900 -tsnetref 2 -nodename at1102xxx > ntsnet: starting 1 worker on at1103.ime.eb.br > /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_rsh > at1103.ime.eb.br -r ssh /usr/local/g03/linda-exe/l302.exel 65536000 > /home/alex/Gau-18733.chk 0 /home/alex/Gau-18733.int 0 > /home/alex/Gau-18733.rwf 0 /home/alex/Gau-18733.d2e 0 > /home/alex/Gau-18733.scr 0 /home/alex/Gau-18732.inp 0 junk.out 0 > +LARGS 5 3 -maxworkers 3 -chdir /home/alex -worker at1:30997 > -workerwait 900 -tsnetref 3 -nodename at1103xxx > ntsnet: exec'ing > /usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/LindaLauncher > /home/alex/tmp/viaExecDataaCXV13 > $ > > After that, the job apparentelly freeze at link l302.exel. > Nothing is running at nodes. > $ps > PID TTY TIME CMD > 15837 pts0 00:00:00 bash > 18731 pts0 00:00:00 g03l > 18732 pts0 00:00:00 g03 > 18733 pts0 00:00:03 l302.exe > 18735 pts0 00:00:00 cLindaLauncher > 18738 pts0 00:00:01 l302.exel > 18739 pts0 00:00:00 ssh > 18740 pts0 00:00:00 ssh > 18741 pts0 00:00:00 ssh > 19034 pts0 00:00:00 ps > > To test the execution I have past the folowing command > line (from ntsnet: starting 1 worker on at1101xxx) > > $/usr/local/g03/linda7.1/intel-linux2.4-rh8/bin/linda_rsh > at1101.ime.eb.br -r ssh /usr/local/g03/linda-exe/l302.exel 65536000 > /home/alex/Gau-18733.chk 0 /home/alex/Gau-18733.int 0 > /home/alex/Gau-18733.rwf 0 /home/alex/Gau-18733.d2e 0 > /home/alex/Gau-18733.scr 0 /home/alex/Gau-18732.inp 0 junk.out 0 > +LARGS 5 1 -maxworkers 3 -chdir /home/alex -worker at1:30997 > -workerwait 900 -tsnetref 1 -nodename at1101.ime.eb.br > failed to look up given name -workerwait > > What can I change to work withou problems? > > Alexander. > From owner-chemistry@ccl.net Tue Oct 25 19:59:00 2005 From: "TJ O Donnell tjo#%#acm.org" To: CCL Subject: CCL: help needed Message-Id: <-29739-051025194813-17188-5EyOrwSab3Xz7iijV9k+mw%a%server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 25 Oct 2005 16:47:33 -0700 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo-#-acm.org] For serious use of linux under Windows, I would recommend VMWare. http://www.vmware.com - look for the Workstation product. It is an excellent product and very reasonably priced - about $185 if I remember correctly. The speed is about 90% of a native linux machine, except for high-speed interactive graphics. As a programming, X-windows and development tool it is great. It works better if you have additional memory so it can have a big chunk all for itself. I use VMWare on my 1Gb laptop every day, with Windows XP and the host, Fedora as the guest operating system. TJ O'Donnell http://www.gnova.com Perry E. Metzger perry^piermont.com wrote: > Sent to CCL by: "Perry E. Metzger" [perry-#-piermont.com] > > "Dr Seth Olsen s.olsen1(_)uq.edu.au" writes: > >>You may find your options are greater if you use something like Cygwin >>under windows. I couldn't get that technical about the description, but >>Cygwin essentially gives you a linux-imitating environment that runs >>under windows. > > > It is a reasonable emulation environment, though you have to recompile > anything you need to use, and the edges are a bit sharp. I use > it when I'm forced to set stuff up in Windows environments -- it is a > lot more productive than the usual Microsoft tools. > > Microsoft also has a similar offering that they give away called > (inexplicably) "Services for Unix". I've heard they're getting rid of > it though. > > Performance under Cygwin will not rival performance on a real Linux > box -- Windows has architectural issues that make it perform pretty > badly in general, and Cygwin is just a POSIX scrim over Windows. > > >>Cygwin is free. I think the site is www.cygwin.org or somesuch. > > > http://www.cygwin.com/ actually. > > Perry> > From owner-chemistry@ccl.net Tue Oct 25 21:41:00 2005 From: "Mark Thompson mark|a|arguslab.com" To: CCL Subject: CCL: A new ArgusLab 4.01 bug fix release is now available Message-Id: <-29740-051025205840-17911-oqEwjiEV4zsx98DZWEnpBg-#-server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 25 Oct 2005 17:58:23 -0700 MIME-Version: 1.0 Sent to CCL by: Mark Thompson [mark*o*arguslab.com] I've just uploaded a new ArgusLab 4.01 installer with a couple of bug fixes: 1. Some bugs in the RMSD code fixed. 2. The installer is fixed to allow the user to install for anyone using the computer (if they have admin priviledges) or for the current user. Apologies for the inconvenience for so many users having to wait for #2 Cheers, Mark -- ---------------------------- Mark Thompson mark/./arguslab.com http://www.arguslab.com ---------------------------- From owner-chemistry@ccl.net Tue Oct 25 22:16:00 2005 From: "Yubo Fan yubofan~~mail.chem.tamu.edu" To: CCL Subject: CCL: cubegen problem in G03 Message-Id: <-29741-051025184157-19540-WvFt4MyVgp7uy6bjdvGOOA(0)server.ccl.net> X-Original-From: "Yubo Fan" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0043_01C5D982.F9C5E8C0" Date: Tue, 25 Oct 2005 16:41:40 -0500 MIME-Version: 1.0 Sent to CCL by: "Yubo Fan" [yubofan{=}mail.chem.tamu.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0043_01C5D982.F9C5E8C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, everyone, I've done some CIS calculations about some chromophores with G03. Then = I've got some problems to generate density transition cube files with = cubegen. I've got some references but the results were calculated with = G94. In G94 #p CIS(read,direct,Nstates=3D2)/3-21G* pop=3Dreg scf=3Ddirect = guess=3D(read,only) density=3D(transition=3D1,check) geom=3Dcheck nosymm = cube=3D(density,full,cards) can generate the cube files based on the previous CIS calculations. BUT, in G03, the keywork cube is not available, so I have to utilize = cubegen program (I guess it's better). In the command line, I input = "cubegen 0 Density=3DSCF test.fchk test.cube 0 h". Is the INPUT correct = compared to G94? If not, what should I type in? Thanks in advance, Yubo =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Yubo Fan Email: yubofan(a)mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-5237 Texas A&M University College Station, TX 77843 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_0043_01C5D982.F9C5E8C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi, everyone,
 
I've done some CIS calculations about = some=20 chromophores with G03. Then I've got some problems to generate density=20 transition cube files with cubegen. I've got some references but the = results=20 were calculated with G94.
 
In G94
 
#p=20 CIS(read,direct,Nstates=3D2)/3-21G* pop=3Dreg scf=3Ddirect = guess=3D(read,only)=20 density=3D(transition=3D1,check) geom=3Dcheck nosymm=20 cube=3D(density,full,cards)
 
can = generate the cube files=20 based on the previous CIS calculations.
 
BUT, in = G03, the keywork=20 cube is not available, so I have to utilize cubegen program (I guess = it's=20 better). In the command line, I input "cubegen 0 Density=3DSCF test.fchk = test.cube=20 0 h". Is the INPUT correct compared to G94? If not, what should I type=20 in?
 
Thanks in=20 advance,
 
Yubo
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr. Yubo=20 Fan           &nbs= p;  =20 Email: yubofan(a)mail.chem.tamu.edu=
Department=20 of Chemistry    Tel:   1-979-845-5237
Texas = A&M=20 University
College Station, TX=20 77843
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
= ------=_NextPart_000_0043_01C5D982.F9C5E8C0-- From owner-chemistry@ccl.net Tue Oct 25 22:51:00 2005 From: "Cory Pye cpye]|[crux.smu.ca" To: CCL Subject: CCL: rigid scan in Gaussian Message-Id: <-29742-051025194809-17152-yZM5MJ7CuxR8oUvQcY8Kpw-,-server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 25 Oct 2005 20:47:56 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye|,|crux.smu.ca] Hello, this setup is inherently asymmetric along the reaction coordinate, although the reactant and product could be the same. Any constraint here would be artificial, but may be adequate for your needs. It reminds be of a water mediated 1,3-hydrogen shift in triazene, see Can J Chem 80 p447 (2002) . If the reactant and product are the same, then you could use a bit of vector algebra and specify the coordinates of the atoms using Cartesians. I don't think that there is an automatic way of doing this. Suppose q1i are the 3D coordinates of the molecule before the shift, and let q1f be the coordinates after. Then q1(l)=(1-l)*q1i + l*q1f are the coordinates along the dimensionless reaction coordinate 0 Hi everyone, > > I need to model a reaction path of hydrogen abstraction, mediated by water > molecule. > A hydrogen from the substrate is transferred to the water molecule and > simultaneously one of the water hydrogens is transferred to the acceptor. I > am interested in the energy along this pathway without reoptimizing the > substrate and the acceptor at every step along the reaction coordinate. The > reaction coordinate is a straight line. > > The Scan keyword (rigid scan) is going to give me a potential surface, not a > potential curve, if I specify the coordinates of the two hydrogens, that are > moving simultaneously, calculating at every coordinate change of the first H > the all the changes for the second H. > > How can I do the calculation in such a way that I have for each change in > the first H distance to the substrate just one change in the distance for > the second hydrogen, without having to resort to multiple single point > calculations? > > Thank you. > Mima Staikova > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye^crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans)