From owner-chemistry@ccl.net Thu Oct 13 03:02:00 2005 From: "Marcel Swart m.swart*few.vu.nl" To: CCL Subject: CCL: RE: Where can you publish articles on software? Message-Id: <-29579-051013025718-16098-55dLAAzdzc30bXnpmLyQUg-.-server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-1-555510697 Date: Thu, 13 Oct 2005 08:56:05 +0200 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Marcel Swart [m.swart|-|few.vu.nl] --Apple-Mail-1-555510697 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Yes, see: Chemistry with ADF G.=A0te=A0Velde, F.M.=A0Bickelhaupt, E.J.=A0Baerends, = C.=A0Fonseca=A0Guerra, =20 S.J.A.=A0van=A0Gisbergen, J.G.=A0Snijders, T.=A0Ziegler Journal of Computational Chemistry, Vol. 22, No. 9, 931-967 (2001) But that was on the scientific aspects of ADF, not merely the technical =20= part. On Oct 13, 2005, at 2:16 AM, John McKelvey jmmckel*|*attglobal.net =20 wrote: > > Sent to CCL by: John McKelvey [jmmckel]-[attglobal.net] > Folks, > > Am I wrong on this: Didn't Tom Ziegler, or someone, publish a nice =20 > article on ADF a while ago? Gave a lot of insight to a very credible = =20 > code!!! > > Cheers, > > John McKelvey > > > Warren DeLano warren_-_delsci.com wrote: > >> 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, =20= >>> and we specifically EXCLUDE program announcements/descriptions from =20= >>> our pages. Programs are not original research, but may be =20 >>> implementations of original research. >>> >> >> This fails to acknowledge the critical enabling role of software in >> computational chemistry and conveys a shockingly dismissive view of =20= >> 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 =20= >>> these item and has been steadily increasing since we eliminated =20 >>> 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 =20 >> 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! = =20 >> 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 =20= >>> 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 = =20 >> of >> abstract algorithms in the form of non-working descriptive =20 >> 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 =20= >> need >> to be appropriately recognized and rewarded through career =20 >> advancement, >> and thus it is not by accident that so many talented scientific =20 >> software >> developers have chosen the private sector over the academic world. =20= >> The >> system of academic credit is largely broken with respect to creation =20= >> of >> quality research software. >> >> While JMCM may indeed have a fine "editorial" policy on this matter, =20= >> 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 =20 >> 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 =20 >> method. >> >> The only way to publish software in a scientifically robust manner is = =20 >> 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 =20= >> what >> a given program allegedly does. What is that called outside of =20 >> 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 = =20 >>> large number of papers on semiempirical methods, but never published = =20 >>> 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 =20= >> 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 = =20 >> . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 =20 >> Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 >> . mailto:warren%x%delsci.com >> >>> -----Original Message----- >>> From: owner-chemistry%x%ccl.net [mailto:owner-chemistry%x%ccl.net] >>> Sent: Tuesday, October 11, 2005 4:46 PM >>> To: Warren DeLano >>> Subject: CCL: W:CCL: Where can you publish articles on software? >>> >>> >>> 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 =20 >>>> technical programmes >>>> >>>>> This is exactly what I think *should* be encouraged! If we look at = =20 >>>>> bioinformatics, the latest issue of "BMC Bioinformatics" has 7 =20 >>>>> software articles (this journal has an impact factor of 5.42); the = =20 >>>>> latest issue of "Bioinformatics" has 9 'Application Notes' (this =20= >>>>> journal has an impact factor of 5.74). There is a real interest in = =20 >>>>> useful software that can make it easier to do science. >>>>> >>> I am the editor of the Journal of Molecular Graphics and Modelling, =20= >>> and we specifically EXCLUDE program announcements/descriptions from =20= >>> our pages. Programs are not original research, but may be =20 >>> implementations of original research. >>> >>> Being a former member of the Dewar group, they certainly published a = =20 >>> large number of papers on semiempirical methods, but never published = =20 >>> any article on AMPAC itself. These programs were even run on just a = =20 >>> few examples of "suitable data of interest"! The algorithm is =20 >>> perhaos >>> >> >> >>> worthy of publication, and the program can certainly be mentioned, =20= >>> but >>> >> >> >>> is not in and of itself worthy of the valuable space in a research =20= >>> journal. >>> >>> Comparison to various other journals with high impact factors is =20 >>> anecdotal at best. The data from JMGM indicate that our IF went =20 >>> DOWN when we included these item and has been steadily increasing =20= >>> since we eliminated them. But that could also have been for a =20 >>> number of other reasons. >>> >>> My 0.02. >>> >>> Regards, Andy Holder >>> >>> -=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-=20 >>> =3D- 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 >>> = -=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 This is automatically added to each message by the mailing = script =20 >>> =3D- To recover the email address of the author of the message, = please =20 >>> change the strange characters on the top line to the %x% sign. You =20= >>> can also> =20 >>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >>> -+-+-+-+-+> >> >> >> >> > > > > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please =20 > change=20> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-=20= > +-+ > > > > =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart(_)few.vu.nl Web http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-1-555510697 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 Yes, see: Chemistry with ADF G.=A0te=A0Velde, F.M.=A0Bickelhaupt, E.J.=A0Baerends, = C.=A0Fonseca=A0Guerra, S.J.A.=A0van=A0Gisbergen, J.G.=A0Snijders, T.=A0Ziegler Journal of Computational Chemistry, Vol. 22, No. 9, 931-967 (2001)=20 But that was on the scientific aspects of ADF, not merely the technical part. On Oct 13, 2005, at 2:16 AM, John McKelvey jmmckel*|*attglobal.net wrote: 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 Warren DeLano warren_-_delsci.com wrote: Sent to CCL by: "Warren DeLano" [warren(~)delsci.com] =20 Sent to CCL by: "Andy Holder" [holdera%umkc.edu] =20 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. =20 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. =20 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. =20 The data from JMGM indicate that our IF went DOWN when we included these item and has been steadily increasing since we eliminated them. =20 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. =20 The algorithm is perhaps worthy of publication, and the program can certainly be mentioned, but is not in =20 =20 and of itself worthy of the valuable space in a research journal. =20 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. =20 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. =20 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. =20 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 =20 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942=20 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren%x%delsci.com =20 =20 -----Original Message----- > From: owner-chemistry%x%ccl.net [mailto:owner-chemistry%x%ccl.net] Sent: Tuesday, October 11, 2005 4:46 PM To: Warren DeLano Subject: CCL: W:CCL: Where can you publish articles on software? Sent to CCL by: "Andy Holder" [holdera%umkc.edu] In reply to: =20 This programme is surely useful, but the editors of =20 research journals =20 would probably not accept it for publication. If this kind =20 of article =20 is acceptable, I guess that many people would produce tons of technical programmes =20 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. =20 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 =20 =20 worthy of publication, and the program can certainly be mentioned, but =20 =20 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 -=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- 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 -=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 This is automatically added to each message by the mailing script =3D-the strange characters on the top line to the %x% sign. You can also> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+-+-+-+-+> =20 -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_message=20Job advertisements: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt= Helvetica=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96 = Papyrusdr. Marcel Swart = Papyrus = OsakaTheoretische Chemie Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands Tel +31-(0)20-5987619 Fax +31-(0)20-5987629 E-mail m.swart(_)few.vu.nl Web http://www.few.vu.nl/~swart = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-1-555510697-- From owner-chemistry@ccl.net Thu Oct 13 04:49:01 2005 From: "Per-Ola Norrby pon(!)kemi.dtu.dk" To: CCL Subject: CCL: Where can you publish articles on software? Message-Id: <-29580-051013044511-13128-w/WLxU45qkX+lpMiT1RWYg~!~server.ccl.net> X-Original-From: Per-Ola Norrby Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Thu, 13 Oct 2005 10:44:59 +0200 Mime-Version: 1.0 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 From owner-chemistry@ccl.net Thu Oct 13 05:32:01 2005 From: "Joop van Lenthe joop[-]chem.uu.nl" To: CCL Subject: CCL: W:How to calculate the BSSE Correction Message-Id: <-29581-051013052540-28693-noSVQVl8G0RhPcVZPphy6A:-:server.ccl.net> X-Original-From: Joop van Lenthe Content-Type: multipart/alternative; boundary=Apple-Mail-29-560874604 Date: Thu, 13 Oct 2005 10:25:29 +0200 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Joop van Lenthe [joop]_[chem.uu.nl] --Apple-Mail-29-560874604 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi I am afraid you misunderstood the paper. You should calculate every molecule in the basis of the whole complex. That means, that for doing the monomer calculculation you start with the dimer calculation. You make sure that the atoms of the other molecule are still there (in the geometry of the dimer) but with zero charge; this is called a ghost. Of course the number of electrons has to be the number of electrons in the monomer you are calculating. I think the massage keyword in GAUSSIAN can be used to do this, but I do not use the program. Joop On Oct 13, 2005, at 5:36, Faisal Rahman s101alif ~~ mail.chem.itb.ac.id wrote: > > Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] > Hi everybody ... > > I'am a newbie here ... > I'am an undergraduate student of Chemistry Department of Bandung > Institute of Technology. I'am doing my Final project, studying > hydrogen bond between DNA Bases and HCl using DFT,MP2 and HF method > using 6-31++G** basis set, using gaussian 03. I Have a problem with > the BSSE correction. I don't know how to calculate it. > For example, I get confused to calculate the interaction energy that > corrected with BSSE of complex adenine and HCl.So what should i do ... > Could anyone tell me ... > I ever read an article about BSSE, It tell that the correction of > interaction energy can be done by calculate every singel molecule with > the basis of other molecule. could anyone give the example of input > file of gaussian to calculate the HCl energy on the basis of adenine > or to calculate adenine on the basis of HCl? > Thank's before ... > I would very approciate it > > > Faisal Rahman > Chemistry Department of Bandung Institute of Technology> To recover the email address of the author of the message, please > change> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > ========================================= Joop van Lenthe Theoretical Chemistry Group Debye Institute, Utrecht University Padualaan 8 3584 CH Utrecht -31-30-2532733 joop===chem.uu.nl ========================================= --Apple-Mail-29-560874604 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Hi I am afraid you misunderstood the paper. You should calculate every molecule in the basis of the whole complex. That means, that for doing the monomer calculculation you start with the dimer calculation. You make sure that the atoms of the other molecule are still there (in the geometry of the dimer) but with zero charge; this is called a ghost. Of course the number of electrons has to be the number of electrons in the monomer you are calculating. I think the massage keyword in GAUSSIAN can be used to do this, but I do not use the program. Joop On Oct 13, 2005, at 5:36, Faisal Rahman s101alif ~~ mail.chem.itb.ac.id wrote: Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] Hi everybody ... I'am a newbie here ... I'am an undergraduate student of Chemistry Department of Bandung Institute of Technology. I'am doing my Final project, studying hydrogen bond between DNA Bases and HCl using DFT,MP2 and HF method using 6-31++G** basis set, using gaussian 03. I Have a problem with the BSSE correction. I don't know how to calculate it. For example, I get confused to calculate the interaction energy that corrected with BSSE of complex adenine and HCl.So what should i do ... Could anyone tell me ... I ever read an article about BSSE, It tell that the correction of interaction energy can be done by calculate every singel molecule with the basis of other molecule. could anyone give the example of input file of gaussian to calculate the HCl energy on the basis of adenine or to calculate adenine on the basis of HCl? Thank's before ... I would very approciate it Faisal Rahman Chemistry Department of Bandung Institute of Technologyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt========================================= Joop van Lenthe Theoretical Chemistry Group Debye Institute, Utrecht University Padualaan 8 3584 CH Utrecht -31-30-2532733 joop===chem.uu.nl ========================================= --Apple-Mail-29-560874604-- From owner-chemistry@ccl.net Thu Oct 13 06:06:00 2005 From: "Michel Petitjean ptitjean*|*itodys.jussieu.fr" To: CCL Subject: CCL: Re(2): Where can you publish articles on software? Message-Id: <-29582-051013052939-29130-ypILetU3Zx/lmJmR7+23lA-,-server.ccl.net> X-Original-From: Michel Petitjean Date: Thu, 13 Oct 2005 11:29:22 +0200 (MEST) 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 From owner-chemistry@ccl.net Thu Oct 13 06:42:00 2005 From: "Konrad Hinsen khinsen .. cea.fr" To: CCL Subject: CCL: W:CCL: Re: Where can you publish articles on software? Message-Id: <-29583-051013053346-30648-eFNcstYRmfpuOYgahVEmUA]~[server.ccl.net> X-Original-From: "Konrad Hinsen" 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 ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Oct 13 07:27:00 2005 From: "Chas Simpson csimpson||hydrogen.cem.uct.ac.za" To: CCL Subject: CCL: W:Re:Test driven development/XP etc. in scientific software development Message-Id: <-29584-051013072334-4054-bZ2YC8oVXe2wfVRmWypjqw^server.ccl.net> X-Original-From: "Chas Simpson" Sent to CCL by: "Chas Simpson" [csimpson_-_hydrogen.cem.uct.ac.za] Thanks to Geoff Hutchison for pointing out my fairly sweeping generalisation on the quality and number of development tools available for Fortran and C/C++. Apologies, I was referring to the testing tools and I'm not really in a position to comment on quality of these products for Fortran or C++. What Im interested in are the testing techniques employed by coders in the CCL. As far as I recall, the likes of Charmm, Gaussian, GAMES-US, Namd, and DL_Poly do not employ unit tests. I could be completely wrong. However, as Geoff pointed out, a lot of packages do provide test simulations to ensure the overall build is correct. None that I know of come with testing mechanisms for the individual critical components, nevermind at the individual function/procedure/method level. My questions stem from the fact that in business software development there is a growing enthusiasm and support for test driven development (see testdriven.com write unit test first, write code so that the unit test passes, refractor, write next test ). I was wondering if this is catching on in the scientific community? Secondly, does anyone actively employ testers, perhaps undergraduate students in academia and fully fledged QA departments in industry? Finally, are other modern software practices being investigated, such as the use of specific software patterns, Agile development (agilemanifesto.org) and Extreme Programming (www.extremeprogramming.org)? With regards to the non-testing related tools (IDEs/source control/code generation etc) I'm interested in which are the most popular and how widely these are employed. Personally, Ive found that some of the IDEs are glorified text editors and hamper development more than anything else. Source control, debugger and compiler integration is often poor or non-existent (another sweeping generalisation?). Apologies if my generalisations caused any offence - none was intended. Thanks, Chas From owner-chemistry@ccl.net Thu Oct 13 08:02:01 2005 From: "Terry Frankcombe T.Frankcombe^chem.leidenuniv.nl" To: CCL Subject: CCL: W:How to calculate the BSSE Correction Message-Id: <-29585-051013074434-21902-LGhwaRQqKfwA6MVOuz86TA_._server.ccl.net> X-Original-From: Terry Frankcombe Content-Type: text/plain; charset=us-ascii Date: Thu, 13 Oct 2005 13:44:11 +0200 Mime-Version: 1.0 Sent to CCL by: Terry Frankcombe [T.Frankcombe_+_chem.leidenuniv.nl] > Hi > I am afraid you misunderstood the paper. You should calculate every > molecule in the basis > of the whole complex. That means, that for doing the monomer > calculculation you start > with the dimer calculation. You make sure that the atoms of the other > molecule are still there > (in the geometry of the dimer) but with zero charge; this is called a > ghost. Of course the number of > electrons has to be the number of electrons in the monomer you are > calculating. I think > the massage keyword in GAUSSIAN can be used to do this, but I do not > use the program. > Joop Not massage. Ghost atoms. Look at the bottom of . > > > > > Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] > > Hi everybody ... > > > > I'am a newbie here ... > > I'am an undergraduate student of Chemistry Department of Bandung > > Institute of Technology. I'am doing my Final project, studying > > hydrogen bond between DNA Bases and HCl using DFT,MP2 and HF method > > using 6-31++G** basis set, using gaussian 03. I Have a problem with > > the BSSE correction. I don't know how to calculate it. > > For example, I get confused to calculate the interaction energy that > > corrected with BSSE of complex adenine and HCl.So what should i do ... > > Could anyone tell me ... > > I ever read an article about BSSE, It tell that the correction of > > interaction energy can be done by calculate every singel molecule with > > the basis of other molecule. could anyone give the example of input > > file of gaussian to calculate the HCl energy on the basis of adenine > > or to calculate adenine on the basis of HCl? > > Thank's before ... > > I would very approciate it > > > > > > Faisal Rahman > > Chemistry Department of Bandung Institute of Technology> To recover the ema il address of the author of the message, please > > change> > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > +-+ > > > > > > > ========================================= > Joop van Lenthe > Theoretical Chemistry Group > Debye Institute, Utrecht University > Padualaan 8 3584 CH Utrecht > -31-30-2532733 > joop!=!chem.uu.nl > ========================================= > > > --Apple-Mail-29-560874604 > Content-Transfer-Encoding: 7bit > Content-Type: text/enriched; > charset=US-ASCII > > Hi > > I am afraid you misunderstood the paper. You should calculate every > molecule in the basis > > of the whole complex. That means, that for doing the monomer > calculculation you start > > with the dimer calculation. You make sure that the atoms of the other > molecule are still there > > (in the geometry of the dimer) but with zero charge; this is called a > ghost. Of course the number of > > electrons has to be the number of electrons in the monomer you are > calculating. I think > > the massage keyword in GAUSSIAN can be used to do this, but I do not > use the program. > > Joop > > On Oct 13, 2005, at 5:36, Faisal Rahman s101alif ~~ > mail.chem.itb.ac.id wrote: > > > > > Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] > > Hi everybody ... > > > I'am a newbie here ... > > I'am an undergraduate student of Chemistry Department of Bandung > Institute of Technology. I'am doing my Final project, studying > hydrogen bond between DNA Bases and HCl using DFT,MP2 and HF method > using 6-31++G** basis set, using gaussian 03. I Have a problem with > the BSSE correction. I don't know how to calculate it. > > For example, I get confused to calculate the interaction energy that > corrected with BSSE of complex adenine and HCl.So what should i do ... > Could anyone tell me ... > > I ever read an article about BSSE, It tell that the correction of > interaction energy can be done by calculate every singel molecule with > the basis of other molecule. could anyone give the example of input > file of gaussian to calculate the HCl energy on the basis of adenine > or to calculate adenine on the basis of HCl? > > Thank's before ... > > I would very approciate it > > > > Faisal Rahman > > Chemistry Department of Bandung Institute of Technologyhttp://www.ccl.net/cgi -bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www .ccl.net/spammers.txt======================================= == > > Joop van Lenthe > > Theoretical Chemistry Group > > Debye Institute, Utrecht University > > Padualaan 8 3584 CH Utrecht > > -31-30-2532733 > > joop!=!chem.uu.nl > > ========================================= > > > > > --Apple-Mail-29-560874604--> > From owner-chemistry@ccl.net Thu Oct 13 08:37:00 2005 From: "Andreas Serr serr!^!theorie.physik.uni-muenchen.de" To: CCL Subject: CCL: W:How to calculate the BSSE Correction Message-Id: <-29586-051013074459-22094-NoVL6820ztFLVAa9994j6w*server.ccl.net> X-Original-From: Andreas Serr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Oct 2005 13:44:53 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Andreas Serr [serr-.-theorie.physik.uni-muenchen.de] Dear Faisal, Joop van Lenthe joop[-]chem.uu.nl wrote: > Hi > I am afraid you misunderstood the paper. You should calculate every > molecule in the basis > of the whole complex. That means, that for doing the monomer > calculculation you start > with the dimer calculation. You make sure that the atoms of the other > molecule are still there > (in the geometry of the dimer) but with zero charge; this is called a > ghost. Of course the number of > electrons has to be the number of electrons in the monomer you are > calculating. I think > the massage keyword in GAUSSIAN can be used to do this, but I do not > use the program. Yes, it is possible like this, but better is to use the ghost atom type: just add "-Bq" after the atom symbol, e.g in a molecule specification (in cartesian coordinates): O-Bq 1.2423 0.2344 0.353 to get an Oxygen ghost atom at that position. Also possible in z-matrix specification. Regards, Andreas > Joop > On Oct 13, 2005, at 5:36, Faisal Rahman s101alif ~~ mail.chem.itb.ac.id > wrote: > >> >> Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] >> Hi everybody ... >> >> I'am a newbie here ... >> I'am an undergraduate student of Chemistry Department of Bandung >> Institute of Technology. I'am doing my Final project, studying >> hydrogen bond between DNA Bases and HCl using DFT,MP2 and HF method >> using 6-31++G** basis set, using gaussian 03. I Have a problem with >> the BSSE correction. I don't know how to calculate it. >> For example, I get confused to calculate the interaction energy >> that corrected with BSSE of complex adenine and HCl.So what should i >> do ... Could anyone tell me ... >> I ever read an article about BSSE, It tell that the correction of >> interaction energy can be done by calculate every singel molecule >> with the basis of other molecule. could anyone give the example of >> input file of gaussian to calculate the HCl energy on the basis of >> adenine or to calculate adenine on the basis of HCl? >> Thank's before ... >> I would very approciate it >> >> >> Faisal Rahman >> Chemistry Department of Bandung Institute of Technology> To recover >> the email address of the author of the message, please change> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- +-+ >> >> >> > ========================================= > Joop van Lenthe > Theoretical Chemistry Group > Debye Institute, Utrecht University > Padualaan 8 3584 CH Utrecht > -31-30-2532733 > joop!=!chem.uu.nl > ========================================= > > Andreas Serr Biological Soft-Matter Theory Sektion Physik - Ludwig-Maximilians-Universitaet Theresienstr. 37, D-80333 Munich, Germany tel: +49-(0)89-2180-4603 / fax: +49-(0)89-2180-4517 room no: 304 / e-mail: serr- -theorie.physik.uni-muenchen.de http://www.theorie.physik.uni-muenchen.de/biophysics/ From owner-chemistry@ccl.net Thu Oct 13 09:12:00 2005 From: "Konrad Hinsen khinsen[*]cea.fr" To: CCL Subject: CCL: W:CCL: Re(2): Where can you publish articles on software? Message-Id: <-29587-051013081622-10956-wwp8ngrHlYsoWuc4MhYpEw() server.ccl.net> X-Original-From: "Konrad Hinsen" 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[a]cea.fr --------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Oct 13 09:46:00 2005 From: "Peter Gannett pgannett#,#hsc.wvu.edu" To: CCL Subject: CCL: Amber calculations with Gaussian Message-Id: <-29588-051013075159-25765-VIGG9D0YaIO6PlWNpvW6TA__server.ccl.net> X-Original-From: "Peter Gannett" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 13 Oct 2005 07:15:51 -0400 Mime-Version: 1.0 Sent to CCL by: "Peter Gannett" [pgannett .. hsc.wvu.edu] XRED/RED will help but antechamber (with the correct options) will do, too. With XRED/RED, I believe you also have to have either gaussian or GAMESS. Pete >>> owner-chemistry!=!ccl.net 10/12 9:27 PM >>> Sent to CCL by: Prashanth Athri [athriprashanth{:}yahoo.com] I believe RED or XRED (w GUI) is free and does whats needed. http://www.u-picardie.fr/labo/lbpd/RED/ --- "Evgeniy Gromov Evgeniy.Gromov##tc.pci.uni-heidelberg.de" wrote: > > Sent to CCL by: Evgeniy Gromov > [Evgeniy.Gromov]|[tc.pci.uni-heidelberg.de] > Dear All, > > I have a question concerning Amber type (molecular > mechanics) > calculations using Gaussian03. Does anybody know > some (free) soft > (except for GaussView) which allows one to specify > automatically > all necessary for Amber input information (i.e. the > type of > hybridization, partial charge etc. for all atoms) in > the format > required by Gaussian. Thanks. > > Best, > Evgeniy > > -- > _______________________________________ > Dr. Evgeniy Gromov > Theoretische Chemie > Physikalisch-Chemisches Institut > Im Neuenheimer Feld 229 > D-69120 Heidelberg > Germany > > Telefon: +49/(0)6221/545263 > Fax: +49/(0)6221/545221 > E-mail: evgeniy:_:tc.pci.uni-heidelberg.de > _______________________________________ > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the __ > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST__ccl.net > or use> > Before posting check wait time for next message at: > http://www.ccl.net> > If your mail bounces from CCL with 5.7.1 error, > check:> > > > __________________________________ Start your day with Yahoo! - Make it your home page! http://www.yahoo.com/r/hshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Oct 13 10:21:00 2005 From: "Sebastian H. Riedel sebastian.riedel.:.mail.uni-wuerzburg.de" To: CCL Subject: CCL: How to calculate the BSSE Correction Message-Id: <-29589-051013082551-11717-DIK9Ju75feG3wVPzXYiR7g**server.ccl.net> X-Original-From: "Sebastian H. Riedel" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01C5CFF7.F560CA00" Date: Thu, 13 Oct 2005 13:13:52 +0200 MIME-Version: 1.0 Sent to CCL by: "Sebastian H. Riedel" [sebastian.riedel#,#mail.uni-wuerzburg.de] This is a multi-part message in MIME format. ------=_NextPart_000_000D_01C5CFF7.F560CA00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi In Gaussian03 you can also use the keyword "counterpoise". =20 http://www.gaussian.com/g_ur/k_counterpoise.htm =20 Here is some sample output from a Counterpoise calculation: =20 Counterpoise: corrected energy =3D -2660.083831739527=20 Counterpoise: BSSE energy =3D 0.003902746890=20 =20 Greetings =20 SEB =20 --------------------------------------------=20 Dipl. Chem. Sebastian H. Riedel=20 Workgroup Prof. Dr. M. Kaupp=20 Institut f=FCr Anorganische Chemie=20 University W=FCrzburg=20 Am Hubland=20 D-97074 W=FCrzburg, Germany=20 =20 Phone: +49-931-888-5495=20 E-mail: sebastian.riedel*o*mail.uni-wuerzburg.de=20 www: http://www-anorganik.chemie.uni-wuerzburg.de/kaupp=20 www: http://www.psichem.de =20 --------------------------------------------=20 -----Urspr=FCngliche Nachricht----- Von: owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net]=20 Gesendet: Donnerstag, 13. Oktober 2005 10:25 An: Riedel, S Betreff: CCL: W:How to calculate the BSSE Correction Hi I am afraid you misunderstood the paper. You should calculate every = molecule in the basis of the whole complex. That means, that for doing the monomer = calculculation you start with the dimer calculation. You make sure that the atoms of the other molecule are still there (in the geometry of the dimer) but with zero charge; this is called a = ghost. Of course the number of=20 electrons has to be the number of electrons in the monomer you are calculating. I think the massage keyword in GAUSSIAN can be used to do this, but I do not use = the program. Joop On Oct 13, 2005, at 5:36, Faisal Rahman s101alif ~~ mail.chem.itb.ac.id wrote: Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] Hi everybody ... I'am a newbie here ... I'am an undergraduate student of Chemistry Department of Bandung = Institute of Technology. I'am doing my Final project, studying hydrogen bond = between DNA Bases and HCl using DFT,MP2 and HF method using 6-31++G** basis set, using gaussian 03. I Have a problem with the BSSE correction. I don't = know how to calculate it. For example, I get confused to calculate the interaction energy that corrected with BSSE of complex adenine and HCl.So what should i do ... = Could anyone tell me ...=20 I ever read an article about BSSE, It tell that the correction of interaction energy can be done by calculate every singel molecule with = the basis of other molecule. could anyone give the example of input file of gaussian to calculate the HCl energy on the basis of adenine or to = calculate adenine on the basis of HCl? Thank's before ... I would very approciate it Faisal Rahman Chemistry Department of Bandung Institute of Technologyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.n= et/ chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt =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 Joop van Lenthe Theoretical Chemistry Group Debye Institute, Utrecht University Padualaan 8 3584 CH Utrecht -31-30-2532733 joop!=3D!chem.uu.nl =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_000D_01C5CFF7.F560CA00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Nachricht
Hi
In=20 Gaussian03 you can also use the keyword = "counterpoise".
 
http://www.gauss= ian.com/g_ur/k_counterpoise.htm
 
Here=20 is some sample output from a Counterpoise = calculation:
 
Counterpoise: corrected energy =3D =20 -2660.083831739527
Counterpoise: BSSE energy = =3D     =20 0.003902746890
 
Greetings
 
SEB
 

--------------------------------------------
Dipl. Chem. Sebastian = H.=20 Riedel
Workgroup Prof. Dr. M. Kaupp
Institut f=FCr Anorganische = Chemie=20
University=20 W=FCrzburg
Am=20 Hubland
D-97074=20 W=FCrzburg, Germany
 
Phone:  +49-931-888-5495
E-mail:=20 sebastian.riedel*o*mail.uni-wuerzburg.de
www:    http://www-an= organik.chemie.uni-wuerzburg.de/kaupp=20
www:    http://www.psichem.de =
--------------------------------------------

-----Urspr=FCngliche Nachricht-----
Von:=20 owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net] =
Gesendet:=20 Donnerstag, 13. Oktober 2005 10:25
An: Riedel, S=20
Betreff: CCL: W:How to calculate the BSSE=20 Correction

Hi
I am afraid you misunderstood the = paper.=20 You should calculate every molecule in the basis
of the whole = complex. That=20 means, that for doing the monomer calculculation you start
with the = dimer=20 calculation. You make sure that the atoms of the other molecule are = still=20 there
(in the geometry of the dimer) but with zero charge; this is = called a=20 ghost. Of course the number of
electrons has to be the number of = electrons=20 in the monomer you are calculating. I think
the massage keyword in = GAUSSIAN=20 can be used to do this, but I do not use the program.
Joop
On = Oct 13,=20 2005, at 5:36, Faisal Rahman s101alif ~~ mail.chem.itb.ac.id = wrote:


Sent to CCL by: "Faisal Rahman" [s101alif ~=20 mail.chem.itb.ac.id]
Hi everybody ...

I'am a newbie here=20 ...
I'am an undergraduate student of Chemistry Department of = Bandung=20 Institute of Technology. I'am doing my Final project, studying = hydrogen bond=20 between DNA Bases and HCl using DFT,MP2 and HF method using = 6-31++G** basis=20 set, using gaussian 03. I Have a problem with the BSSE correction. I = don't=20 know how to calculate it.
For example, I get confused to = calculate the=20 interaction energy that corrected with BSSE of complex adenine and = HCl.So=20 what should i do ... Could anyone tell me ...
I ever read an = article=20 about BSSE, It tell that the correction of interaction energy can be = done by=20 calculate every singel molecule with the basis of other molecule. = could=20 anyone give the example of input file of gaussian to calculate the = HCl=20 energy on the basis of adenine or to calculate adenine on the basis = of=20 HCl?
Thank's before ...
I would very approciate = it


Faisal=20 Rahman
Chemistry Department of Bandung Institute of=20 = Technologyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.n= et/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt
<= ?smaller>=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
Joop=20 van Lenthe
Theoretical Chemistry Group
Debye Institute, Utrecht=20 University
Padualaan 8 3584 CH=20 = Utrecht
-31-30-2532733
joop!=3D!chem.uu.nl
=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_000D_01C5CFF7.F560CA00-- From owner-chemistry@ccl.net Thu Oct 13 10:56:01 2005 From: "Konrad Hinsen khinsen*_*cea.fr" To: CCL Subject: CCL: W:CCL: W:Re:Test driven development/XP etc. in scientific software devel Message-Id: <-29590-051013083124-12361-Uw5pb4pgaQplz2BPpc2ybQ[A]server.ccl.net> X-Original-From: "Konrad Hinsen" Sent to CCL by: "Konrad Hinsen" [khinsen_+_cea.fr] On Oct 13, 2005, at 13:30, Chas Simpson csimpson||hydrogen.cem.uct.ac.za wrote: > What Im interested in are the testing techniques employed by coders in the CCL. As far > as I recall, the likes of Charmm, Gaussian, GAMES-US, Namd, and DL_Poly do ... > My questions stem from the fact that in business software development there is a growing > enthusiasm and support for test driven development (see testdriven.com write unit test > first, write code so that the unit test passes, refractor, write next test ). I was wondering > if this is catching on in the scientific community? Secondly, does To the best of my knowledge, such techniques are still marginal in the scientific community. One reason is that most big projects (such as the ones you mention) were started before test-driven development became a routine technique. Retrofitting unit tests to existing code would be an enormous amount of work with uncertain payoff, so I don't expect it to happen. But ignorance of the techniques is perhaps the most important reason. > fully fledged QA departments in industry? Finally, are other modern software practices being > investigated, such as the use of specific software patterns, Agile development > (agilemanifesto.org) and Extreme Programming (www.extremeprogramming.org)? Extreme programming is for full-time programmers in development teams; by its very design it requires at least to programmers who work in close collaboration. I don't expect that situation to be common in scientific environments, where development teams are small and work attitudes are more individualistic. Agile programming is similar in being aimed at big teams, and moreover involving customers. In scientific applications, there is no such strict division between developers and users. Software patterns are a different beast, as they can be used at any scale. With the increasing popularity of OO techniques, I expect to see pattern awareness as well in the scientific community. > Personally, Ive found that some of the IDEs are glorified text editors and hamper Glorified but also limiting. The average IDE adds some compiler integration at the price of less sophisticated basic editing functions. Personally, I use Emacs and jEdit. Both are general-purpose programmable editors with support for specific programming languages and some debugging support. Both are cross-platform as well, which is rarely true for IDEs. I have tried a few IDEs, but have never been convinced by any of them. Even if an IDE is good, it is usually limited to one language - for those who use several, that means several different IDEs as well. -- --------------------------------------------------------------------- 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 --------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Oct 13 11:31:00 2005 From: "Tanja van Mourik t.vanmourik++ucl.ac.uk" To: CCL Subject: CCL: W:How to calculate the BSSE Correction Message-Id: <-29591-051013090341-22503-4mi0Onry655IZSnmntEcdA||server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 13 Oct 2005 14:02:05 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [t.vanmourik++ucl.ac.uk] Hi Faisal, With Gaussian 03 one can actually simply use the "Counterpoise" keyword (Massage was used in older versions of Gaussian), see http://www.gaussian.com/g_ur/k_counterpoise.htm This also allows one to do counterpoise-corrected geometry optimisations. It's really easy to use; you basically just have to specify the different fragments, see the Gaussian manual. Hope that helps, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik%a%ucl.ac.uk London WC1H 0AJ, UK home: tanja%a%van-mourik.me.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ================================================================= > I am afraid you misunderstood the paper. You should calculate every > molecule in the basis > of the whole complex. That means, that for doing the monomer > calculculation you start > with the dimer calculation. You make sure that the atoms of the other > molecule are still there > (in the geometry of the dimer) but with zero charge; this is called a > ghost. Of course the number of > electrons has to be the number of electrons in the monomer you are > calculating. I think > the massage keyword in GAUSSIAN can be used to do this, but I do not > use the program. > Joop > On Oct 13, 2005, at 5:36, Faisal Rahman s101alif ~~ mail.chem.itb.ac.id > wrote: > > > > > Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] > > Hi everybody ... > > > > I'am a newbie here ... > > I'am an undergraduate student of Chemistry Department of Bandung > > Institute of Technology. I'am doing my Final project, studying > > hydrogen bond between DNA Bases and HCl using DFT,MP2 and HF method > > using 6-31++G** basis set, using gaussian 03. I Have a problem with > > the BSSE correction. I don't know how to calculate it. > > For example, I get confused to calculate the interaction energy that > > corrected with BSSE of complex adenine and HCl.So what should i do ... > > Could anyone tell me ... > > I ever read an article about BSSE, It tell that the correction of > > interaction energy can be done by calculate every singel molecule with > > the basis of other molecule. could anyone give the example of input > > file of gaussian to calculate the HCl energy on the basis of adenine > > or to calculate adenine on the basis of HCl? > > Thank's before ... > > I would very approciate it > > > > > > Faisal Rahman > > Chemistry Department of Bandung Institute of Technology> To recover the email address of the author of the message, please > > change> > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > +-+ > > > > > > > ========================================= > Joop van Lenthe > Theoretical Chemistry Group > Debye Institute, Utrecht University > Padualaan 8 3584 CH Utrecht > -31-30-2532733 > joop!=!chem.uu.nl > ========================================= > > > --Apple-Mail-29-560874604 > Content-Transfer-Encoding: 7bit > Content-Type: text/enriched; > charset=US-ASCII > > Hi > > I am afraid you misunderstood the paper. You should calculate every > molecule in the basis > > of the whole complex. That means, that for doing the monomer > calculculation you start > > with the dimer calculation. You make sure that the atoms of the other > molecule are still there > > (in the geometry of the dimer) but with zero charge; this is called a > ghost. Of course the number of > > electrons has to be the number of electrons in the monomer you are > calculating. I think > > the massage keyword in GAUSSIAN can be used to do this, but I do not > use the program. > > Joop > > On Oct 13, 2005, at 5:36, Faisal Rahman s101alif ~~ > mail.chem.itb.ac.id wrote: > > > > > Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] > > Hi everybody ... > > > I'am a newbie here ... > > I'am an undergraduate student of Chemistry Department of Bandung > Institute of Technology. I'am doing my Final project, studying > hydrogen bond between DNA Bases and HCl using DFT,MP2 and HF method > using 6-31++G** basis set, using gaussian 03. I Have a problem with > the BSSE correction. I don't know how to calculate it. > > For example, I get confused to calculate the interaction energy that > corrected with BSSE of complex adenine and HCl.So what should i do ... > Could anyone tell me ... > > I ever read an article about BSSE, It tell that the correction of > interaction energy can be done by calculate every singel molecule with > the basis of other molecule. could anyone give the example of input > file of gaussian to calculate the HCl energy on the basis of adenine > or to calculate adenine on the basis of HCl? > > Thank's before ... > > I would very approciate it > > > > Faisal Rahman > > Chemistry Department of Bandung Institute of Technologyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt========================================= > > Joop van Lenthe > > Theoretical Chemistry Group > > Debye Institute, Utrecht University > > Padualaan 8 3584 CH Utrecht > > -31-30-2532733 > > joop!=!chem.uu.nl > > ========================================= > > > > > --Apple-Mail-29-560874604--> > > > From owner-chemistry@ccl.net Thu Oct 13 12:07:00 2005 From: "raquel crespin rache97.^^.yahoo.com" To: CCL Subject: CCL: W:How to calculate the BSSE Correction Message-Id: <-29592-051013100148-17036-xapZ3yDRNfbhWXKW6Xwaog^^server.ccl.net> X-Original-From: raquel crespin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 13 Oct 2005 07:01:38 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: raquel crespin [rache97##yahoo.com] Faisal, You can calculate BSSE with gaussian03 using the counterpoise=n, where n is the number of monomers in the calculation. For these calculations the energy of each monomer is evaluated in the basis of the whole system based in the method of Boys and Bernardi (Mol. Phys. 19, 553 (1970)). Example: %nprocl=4 %mem=400MB %chk=t_cp #b3lyp/cc-pvtz counterpoise=3 t 0 1 O 1 O 1 oo 2 O 2 oo 1 60 .0 3 H 1 oh 3 hoo 2 0.0 0 1 H 2 oh 1 hoo 3 0.0 0 2 H 3 oh 2 hoo 1 0.0 0 3 H 1 ho 2 oho 3 d1 0 1 H 2 ho 3 oho 1 d2 0 2 H 3 ho 1 oho 2 d2 0 3 oo 2.7873 oh 0.9771 hoo 78.2005 ho 0.9609 oho 113.8022 d1 112.335 d2 -113.7495 Best regards Rachel --- "Faisal Rahman s101alif ~~ mail.chem.itb.ac.id" wrote: > > Sent to CCL by: "Faisal Rahman" [s101alif ~ > mail.chem.itb.ac.id] > Hi everybody ... > > I'am a newbie here ... > I'am an undergraduate student of Chemistry > Department of Bandung Institute of Technology. I'am > doing my Final project, studying hydrogen bond > between DNA Bases and HCl using DFT,MP2 and HF > method using 6-31++G** basis set, using gaussian 03. > I Have a problem with the BSSE correction. I don't > know how to calculate it. > For example, I get confused to calculate the > interaction energy that corrected with BSSE of > complex adenine and HCl.So what should i do ... > Could anyone tell me ... > I ever read an article about BSSE, It tell that the > correction of interaction energy can be done by > calculate every singel molecule with the basis of > other molecule. could anyone give the example of > input file of gaussian to calculate the HCl energy > on the basis of adenine or to calculate adenine on > the basis of HCl? > Thank's before ... > I would very approciate it > > > Faisal Rahman > Chemistry Department of Bandung Institute of > Technology > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the (0) > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST(0)ccl.net > or use> > Before posting check wait time for next message at: > http://www.ccl.net> > If your mail bounces from CCL with 5.7.1 error, > check:> > > > __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From owner-chemistry@ccl.net Thu Oct 13 12:42:01 2005 From: "Pedro Salvador perico~!~stark.udg.es" To: CCL Subject: CCL: W:How to calculate the BSSE Correction Message-Id: <-29593-051013102532-31212-9OeGQDXYSB7/5Iq4tU1rtQ{=}server.ccl.net> X-Original-From: Pedro Salvador Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 13 Oct 2005 15:06:51 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Pedro Salvador [perico__stark.udg.es] If you have gaussian03 you can use the "Counterpoise" keyword in order to obtain the CP-corrected total energy and interction energy(also you can optimize the total cp-corrected energy, etc..) Pedro On Wed, 12 Oct 2005, Faisal Rahman s101alif ~~ mail.chem.itb.ac.id wrote: > > Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] > Hi everybody ... > > I'am a newbie here ... > I'am an undergraduate student of Chemistry Department of Bandung Institute of Technology. I'am doing my Final project, studying hydrogen bond between DNA Bases and HCl using DFT,MP2 and HF method using 6-31++G** basis set, using gaussian 03. I Have a problem with the BSSE correction. I don't know how to calculate it. > For example, I get confused to calculate the interaction energy that corrected with BSSE of complex adenine and HCl.So what should i do ... Could anyone tell me ... > I ever read an article about BSSE, It tell that the correction of interaction energy can be done by calculate every singel molecule with the basis of other molecule. could anyone give the example of input file of gaussian to calculate the HCl energy on the basis of adenine or to calculate adenine on the basis of HCl? > Thank's before ... > I would very approciate it > > > Faisal Rahman > Chemistry Department of Bandung Institute of Technology> > > From owner-chemistry@ccl.net Thu Oct 13 13:16:00 2005 From: "Perry E. Metzger perry-$-piermont.com" To: CCL Subject: CCL: W:Re:Test driven development/XP etc. in scientific software development Message-Id: <-29594-051013113832-12209-rGpBYstNKShNqp4m6kf/3Q---server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Thu, 13 Oct 2005 11:38:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry ~~ piermont.com] "Chas Simpson" writes: > With regards to the non-testing related tools (IDEs/source > control/code generation etc) I'm interested in which are the most > popular and how widely these are employed. Personally, Ive found > that some of the IDEs are glorified text editors and hamper > development more than anything else. Source control, debugger and > compiler integration is often poor or non-existent (another sweeping > generalisation?). I've already said enough about IDEs, but you bring up source control systems, and I don't think those have been discussed here recently. As with some of my other messages, I would like to make it clear that this message is not intended for people who are mere users of computational chemistry systems. It is intended for those of you who write them. A good source control system (sometimes called a revision control system) is a critical part of modern software development. If you have just one developer involved in a project, source control allows you to stop keeping track of versions and concentrate solely on the programming. With multiple developers, a good source control infrastructure can become a major communications tool among the project members as well as a method of assuring a consistent source base. This is a quick dump of my brain on this topic. Many of you are first and foremost chemists and not computer scientists, so let me begin by explaining what a source control system is. A source control system is a way of tracking all the changes you have ever made to a set of files. Those files could be sources for your computational chemistry system, a bunch of web pages, your lab notes, a set of PDB files, some paper you are collaborating on with co-authors, anything at all really. In a source control system, every time you make a change to a file (and are reasonably happy with it) you do a "check in" -- you tell the system "here is a new version of this file, please remember it for me". Typically every version of a file gets a version number of some sort, and, here is the nice part, you can ask for a copy of any previous version of a file. Typically, you also supply a log message every time you check in a new version of a file, so that later on you can remember (or, if someone else made the change, learn) why the change was made. Check-ins are also called "commits" in some systems, by analogy to a database commit -- i.e. they are a point at which you are committing a change to the source database. Such systems were originally developed to manage source code, but as I said, they are often useful in other contexts. It is not entirely obvious to the amateur why you would want such a thing, so let me explain the motivation a bit. Lets say you're writing a paper and you decide you don't need some section and you remove it. Later, maybe even months or years later, you realize you would like to get that section back, if only to steal some of the language for another document. If you used a source control system, you could retrieve that old version. If you did not, you have to rely on whether you saved a copy of the old version, try to remember where it might be, etc. Lets say you are writing a program. You release a version, and some people note that there are bugs in it, and you fix them, and release a new version. Then, people say "hey, between version 1.4 and 1.5, you somehow broke this other feature." You then wonder "gee, what exactly did I do between version 1.4 and 1.5 that could have done that?" With a source control system, you can just ask the machine to tell you what you did between various revisions and look at them. You can even revert changes that turned out to be bad ideas. Now, for both of these things, you could carefully save a copy of your work every day, in some huge set of subdirectories, with copious notes attached to what every version was, but that gets very very tedious and people will not, in practice, actually do such a thing. Also, if you do things by hand, the machine can't actually help you do things like automatically keeping multiple branches synchronized (see below.) As chemists, most of you are familiar with the notion of a lab notebook as an object that is never modified -- you keep putting new things in a lab notebook, but you have the pages numbered and the notebook exists as an indelible record of all your work. A source control system provides such a thing, in a sense, in the electronic world -- dutifully saving all intermediate versions of what you did so they can be later be fully referred to. Changes go in and they remain in, forever. The system faithfully records the actual history of all changes ever made to the files under control. It is a tool that must be used for a while to understand the depth of its utility. Here is another example. Lets say you have several versions of a program out. Lets say you have a user community who have bought version 1 of your program. Meanwhile you are working on the not-yet-released version 2, but you still need to sometimes give bug fixes to the users who only are on version 1. (Think of Microsoft, who have to send you patches for Windows XP even as they work on Windows Vista.) You can, in a good source control system, maintain multiple different branches of development of your program, and, in the snazziest systems, automatically pull changes between them on request. When you do a release, you branch your system, and you don't have to keep track of what is in the old version, the newer version and the development version of the system -- the source control system keeps track of it for you. If a bug is found in the released version, you can make a new revision *on the branch* to fix it, or (also interestingly) make a revision in the development line, and request that the system automatically update the branch with that particular fix, with the system assisting you in remembering which fixes have been "pulled up" to the branch and which have not. As source code control systems have grown over the years, they've gained all sorts of features beyond merely storing code. For example, one source repository I've dealt with for managing a web site has a script that automatically ran when commits were made to update the site from the source files. If you, say, fixed the spelling of something on 25 pages, and then did a commit, you didn't need to take further action -- the web site simply updated automatically. A typical modern source control system provides lots of hooks for scripts written in languages like Bourne shell, perl, etc., to be run before a commit is accepted (for instance, to make sure it conforms to particular coding standards or that the user has permission to make changes to a particular file), after a commit is accepted, etc. With such mechanisms, all sorts of very interesting "side effects" to commits become possible, like running your test suite automatically every time a commit happens, or sending mail to all the other developers when commits happen, etc. By the way, I'm quite serious in saying that source code control systems are valuable in managing things like a book you are writing, web sites, paperwork in a law practice, you name it. Once you have gotten used to them, they become an amazingly valuable tool for tracking information over many years. Okay, enough of an introduction. You probably want to know a bit more now about what source control systems are out there and which one you might try using. There are several different major "styles" of source control system. First, there are very old school systems like SCCS (the first real source control system I'm aware of, now available in an open source clone, though I'm not sure anyone rational would want it any more except for reading old SCCS repositories), RCS (which is open source), and similar systems. Such systems don't really do terribly much. RCS is a typical example -- when you use RCS, there is a subdirectory in every directory of source code you manage named (funnily enough) "RCS". Every file being managed in the directory has a corresponding database file in the RCS directory -- for example, a file named "code.c" would also have a file called RCS/code.c,v associated with it that stored all the old versions of the file. You check in a new version of a file by using the self contained "ci" program, retrieve an old version with the "co" program, etc. The system really just manipulates a couple of files locally with every command. It is straightforward, easy to understand, and not very flexible if you have a large project with lots of developers associated with it. Systems like RCS and SCCS are largely obsolete for big software development projects, though I do use RCS for managing a few config files on my systems where CVS or SVN would be too heavyweight. Second, there is the CVS paradigm, which is also largely followed by newer systems like Subversion (SVN). In this source control paradigm, you maintain a "repository" that contains the entire set of sources associated with a system, and developers check out, modify and check in sources to the repository, typically from remote systems using network protocols like ssh as the transport. I happen to work part of the time on an open source operating system called NetBSD, and NetBSD is managed in a big CVS repository. The repository sits physically on a machine in San Francisco, but developers do work on their local boxes around the world. If I want to "check out" the latest version of the sources, I run a command that connects to the CVS server and downloads all the changes that have been made since I last updated. If I am editing a part of the code and someone else changes the file I'm working on, the system automatically merges their changes into my local version of the file. If it can't merge the changes in because they conflict with my own work, it alerts me so I can take manual action to merge the changes. Every time someone checks in a change to the repository, an email message with what they've changed and their log message gets sent to the full set of developers, acting as a coordination mechanism within the project. CVS, which is open source, is probably the world's most popular source control system right now, though it is getting a bit old, and has certain design defects that get annoying after a while. Subversion (also known as SVN) is a newer open source source control system that is in a lot of ways much better than CVS, and if someone is starting > from scratch, I recommend looking at it. CVS follows a centralized paradigm for source management in which there is a single true copy of the canonical sources on the repository system. A different paradigm was pioneered by Larry McVoy's "Bitkeeper" (a commercial product) which allows groups of developers to maintain very disparate sets of source trees that are automatically merged into each other over the network when the various developers wish to do merges. I won't get too deeply into this way of working because I have to admit I don't like it much so I'm not a good spokesman for it, but many people seem to like the mechanism a lot -- enough so that there are now several open source source control systems that follow this model, such as arch and monotone. Lots of people seem to really like them, so it is probably a mistake to pay terribly much attention to my prejudice against such systems. You may have noticed that I've mentioned a number of open source systems and not many commercial ones. That's for a good reason -- the open source systems are usually better than the commercial ones these days, or are at worst as good as them. For completeness, though, I should mention the commercial ones. Most importantly, what to avoid: Microsoft's Visual Source Safe is garbage. I don't know how else to say that. It is buggy, horribly misbegotten and has not been maintained for years. Even Microsoft does not use it for their own work (I believe they may use Perforce -- I'm not entirely sure if I remember that right.) I cannot stress enough that there is no excuse on earth for using it. There are some partisans for Rational's "ClearCase" product but I really don't like it much and it requires heroic efforts to administer. ClearCase operates by pretending to be a file system and noticing every write you make to a file, so it "automatically" versions everything. Unfortunately, it turns out that this is not a particularly easy trick to accomplish. As I said, I try to avoid it. It is also pretty expensive considering that it doesn't seem to work as well as simpler and easier systems. Perforce and Bitkeeper are both decent products, with Perforce being more in the RCS/CVS style and Bitkeeper being the origin of the distributed model. What do I use? Some projects I work on picked CVS years ago and there is a lot of inertia about changing, so we use CVS for those. Newer projects I deal with usually use Subversion, which is a very nice piece of software. For very small (one or two files) projects of my own that only I touch, I sometimes use RCS. Perry From owner-chemistry@ccl.net Thu Oct 13 13:51:01 2005 From: "Victor Manuel Rosas-Garcia quimico69(_)yahoo.com" To: CCL Subject: CCL: W:How to calculate the BSSE Correction Message-Id: <-29595-051013114322-14326-7ybO2v8PY+5DtRaY50pQDQ],[server.ccl.net> X-Original-From: Victor Manuel Rosas-Garcia Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 13 Oct 2005 07:43:16 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Victor Manuel Rosas-Garcia [quimico69 * yahoo.com] Dear Faisal, Try this page: http://qcl.theochem.tu-muenchen.de/qcl/help/counterpoise_e.html I have found it useful. Have a nice day! --- "Faisal Rahman s101alif ~~ mail.chem.itb.ac.id" wrote: > > Sent to CCL by: "Faisal Rahman" [s101alif ~ mail.chem.itb.ac.id] > Hi everybody ... > > I'am a newbie here ... > I'am an undergraduate student of Chemistry Department of Bandung Institute of > Technology. I'am doing my Final project, studying hydrogen bond between DNA > Bases and HCl using DFT,MP2 and HF method using 6-31++G** basis set, using > gaussian 03. I Have a problem with the BSSE correction. I don't know how to > calculate it. > For example, I get confused to calculate the interaction energy that > corrected with BSSE of complex adenine and HCl.So what should i do ... Could > anyone tell me ... > I ever read an article about BSSE, It tell that the correction of interaction > energy can be done by calculate every singel molecule with the basis of other > molecule. could anyone give the example of input file of gaussian to > calculate the HCl energy on the basis of adenine or to calculate adenine on > the basis of HCl? > Thank's before ... > I would very approciate it > Victor M. Rosas García, PhD Coordinador del Posgrado en Ciencias Facultad de Ciencias Quimicas, UANL e-mail: quimico69^_^yahoo.com Tel: (81) 8329-4010 ext. 6253 Fax: (81) 8376-5375 __________________________________ Yahoo! Music Unlimited Access over 1 million songs. Try it free. http://music.yahoo.com/unlimited/ From owner-chemistry@ccl.net Thu Oct 13 14:27:01 2005 From: "Ivanciuc, Ovidiu I. oiivanci%%UTMB.EDU" To: CCL Subject: CCL: Where can you publish articles on software? Message-Id: <-29596-051013121016-30110-Fbx80C5mJa6X5Wl7w61t4Q^^^server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Thu, 13 Oct 2005 11:10:13 -0500 MIME-Version: 1.0 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 From owner-chemistry@ccl.net Thu Oct 13 15:02:00 2005 From: "Evgeniy Gromov Evgeniy.Gromov=-=tc.pci.uni-heidelberg.de" To: CCL Subject: CCL: Amber calculations with Gaussian 2 Message-Id: <-29597-051013123845-13629-Qx/8eilJSJNHhUaJwHX+eQ(~)server.ccl.net> X-Original-From: Evgeniy Gromov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 13 Oct 2005 18:38:38 +0200 MIME-Version: 1.0 Sent to CCL by: Evgeniy Gromov [Evgeniy.Gromov(~)tc.pci.uni-heidelberg.de] Thank you Prashanth and Peter for your reply to my question. I never heard about RED and it is good you told me about that nice soft which I might use in the future. But unfortunately RED seems to be not suitable in my present case. The point is that my system is quit big (about 2000 atoms) and I cannot perform any kind of ab initio calculation to find with RED parameters required for Amber. My system is a protein and I thought that it was possible to appropriate each atom in my system corresponding "Amber parameters" basing on the known information (data base) for amino acids. I tried to do this with antechamber but what I got did not look like the format required by Gaussian for performing Amber type calculations. Maybe one needs to use some proper (correct) options as Peter pointed in his message. If you (or somebody else) know these options I will very appreciate this information. My final aim is to perform geometry optimization using ONION (AMBER/HF) scheme. In principle one could use UFF instead of Amber. In this case it is not necessary to specify partial charges, hybridization etc. as in the case of Amber. But I heard that in the case of proteins Amber was better than UFF. Is the last true ?! Best, Evgeniy Peter Gannett pgannett#,#hsc.wvu.edu wrote: > Sent to CCL by: "Peter Gannett" [pgannett .. hsc.wvu.edu] > XRED/RED will help but antechamber (with the correct options) will do, > too. With XRED/RED, I believe you also have to have either gaussian or > GAMESS. > > Pete > > >>>>owner-chemistry]^[ccl.net 10/12 9:27 PM >>> > > > Sent to CCL by: Prashanth Athri [athriprashanth{:}yahoo.com] > I believe RED or XRED (w GUI) is free and does whats > needed. > > http://www.u-picardie.fr/labo/lbpd/RED/ > > --- "Evgeniy Gromov > Evgeniy.Gromov##tc.pci.uni-heidelberg.de" > wrote: > > >>Sent to CCL by: Evgeniy Gromov >>[Evgeniy.Gromov]|[tc.pci.uni-heidelberg.de] >>Dear All, >> >>I have a question concerning Amber type (molecular >>mechanics) >>calculations using Gaussian03. Does anybody know >>some (free) soft >>(except for GaussView) which allows one to specify >>automatically >>all necessary for Amber input information (i.e. the >>type of >>hybridization, partial charge etc. for all atoms) in >>the format >>required by Gaussian. Thanks. >> >>Best, >>Evgeniy >> -- _______________________________________ Dr. Evgeniy Gromov Theoretische Chemie Physikalisch-Chemisches Institut Im Neuenheimer Feld 229 D-69120 Heidelberg Germany Telefon: +49/(0)6221/545263 Fax: +49/(0)6221/545221 E-mail: evgeniy/./tc.pci.uni-heidelberg.de _______________________________________ From owner-chemistry@ccl.net Thu Oct 13 16:13:00 2005 From: "john furr john.furr],[gmail.com" To: CCL Subject: CCL: W:Re:Test driven development/XP etc. in scientific software development Message-Id: <-29598-051013152331-24927-DRbNs6GNFt1nKSTy+FDKYw]|[server.ccl.net> X-Original-From: john furr Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Oct 2005 15:23:25 -0400 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr---gmail.com] A large part of your question is a matter of taste. Software can be designed well in a variety of fashions. There is no perfect way. It really depends on the stage of development your software is at. Is it still just you working on it? How big is your team? Do you have a budget? Are you a start up, an academic, or a member of a large software development firm? One size does not fit all situations. However I can assure you that the tools to do development in C++ are equal to or greater than other languages. Most of the financial institutions code with C++. C++ code is used in a variety of mission critical places. Is C++ the end all be all? Nope, no language is. When it comes to language choice I think a person should consider the ultimate goals of the project. If the code is to be used (and maintained) for years then I advise you to stay with a common language with a proven track record of industry use. If you want to write a standalone program for use in your research lab then by all means write it in what ever language you want. One of the more important lessons I am learning with Dynamol is that on large projects you need to keep the code as modular as possible. In essence I firmly believe that you should do your best to separate interface code from application code. Now to answer your question from my perspective. Tools I personally on Dynamol development: 1) Kdevelop ( for quick stuff I use vi ) 2) Visual C++ 2003 3) Troll Tech QT framework. 4) Heavy use of C++ STL 5) I very seldom use a debugger. 6) Ashamedly I don't regularly use a version control. This is starting to change and I will probably use Subversion. 7) Routine UNIX scripting tools (awk, grep, sed, etc) 8) My Linux to Windows conversion environment is Ruby driven. I don't currently use unit module tests for all of my modules but as Dynamol grows I will certainly have to employ these tactics. I will probably never side with Extreme programming. I think it is a waste of resources. But others can run their companies as they see fit. I do favor agile development, but I think testdriven is really more of a BUZZ word at this time. My main points are it depends on YOUR project. I would love the resources to develop Dynamol like (**cough** Microsoft **cough**), but I don't have said resources. I make do with what I have at the time and strive to keep the code lean, clean, and fast. Ignore the hype and treat your project like your baby and you will be able to determine what the right tools, language, OS, etc. are for you. Don't spend to much time worrying about what others say or do. We could flame about FORTRAN/C++/Ruby/Python until the end of time or we can all write software and let the individuals work out which tool choice is right for their job. Oh one last thing. Learn a few languages. It will make you a much better programmer. Just my 2 (perhaps 4) cents worth. John Furr Dynamol Inc. (518)-423-5190 email: john.furr###gmail.com http://www.dynamol.com On 10/13/05, Chas Simpson csimpson||hydrogen.cem.uct.ac.za wrote: > > Sent to CCL by: "Chas Simpson" [csimpson_-_hydrogen.cem.uct.ac.za] > Thanks to Geoff Hutchison for pointing out my fairly sweeping generalisation on the quality and number of development tools available for Fortran and C/C++. Apologies, I was referring to the testing tools and I'm not really in a position to comment on quality of these products for Fortran or C++. > > What Im interested in are the testing techniques employed by coders in the CCL. As far as I recall, the likes of Charmm, Gaussian, GAMES-US, Namd, and DL_Poly do not employ unit tests. I could be completely wrong. However, as Geoff pointed out, a lot of packages do provide test simulations to ensure the overall build is correct. None that I know of come with testing mechanisms for the individual critical components, nevermind at the individual function/procedure/method level. > > My questions stem from the fact that in business software development there is a growing enthusiasm and support for test driven development (see testdriven.com write unit test first, write code so that the unit test passes, refractor, write next test ). I was wondering if this is catching on in the scientific community? Secondly, does anyone actively employ testers, perhaps undergraduate students in academia and fully fledged QA departments in industry? Finally, are other modern software practices being investigated, such as the use of specific software patterns, Agile development (agilemanifesto.org) and Extreme Programming (www.extremeprogramming.org)? > > With regards to the non-testing related tools (IDEs/source control/code generation etc) I'm interested in which are the most popular and how widely these are employed. Personally, Ive found that some of the IDEs are glorified text editors and hamper development more than anything else. Source control, debugger and compiler integration is often poor or non-existent (another sweeping generalisation?). > > Apologies if my generalisations caused any offence - none was intended. > > Thanks, > > Chas> > > > From owner-chemistry@ccl.net Thu Oct 13 17:20:00 2005 From: "Spencer Ericksen spencer_ericksen!^!hotmail.com" To: CCL Subject: CCL: partial charge fitting - free QM package Message-Id: <-29599-051013135237-22981-xceIf6IsKGpvsqaPhK/SDQ;;server.ccl.net> X-Original-From: "Spencer Ericksen" Content-Type: text/plain; format=flowed Date: Thu, 13 Oct 2005 17:05:21 +0000 Mime-Version: 1.0 Sent to CCL by: "Spencer Ericksen" [spencer_ericksen**hotmail.com] Hello CCLers: I am constructing drug molecules to dock into a receptor using molecular mechanics forcefield representation of atoms. The drug molecules were built in Sybyl and partial charges were first added using the Gasteiger-Marsili charges by default. I then performed an AM1 MOPAC calculation to derive Mulliken charges which were differed to some extent. I do not currently have a program to perform higher level ab initio calculations from which tto derive better charges. Where may I obtain a free QM program that performs ab initio calculations with acceptable basis sets for small organic molecules from which to derive MM partial charges? Are higher level QM calculations necessary to fit a good set of partial charges--even when solvent effects are not included in typical calculations (gas phase)? What is the most common technique for partial charge assignment is used for high-throughput in silico screening by docking when millions of ligands are used? Spencer Ericksen Dept. of Physiology UW-Madison ericksen .. physiology.wisc.edu From owner-chemistry@ccl.net Thu Oct 13 20:26:00 2005 From: "Mark Thompson mark]~[arguslab.com" To: CCL Subject: CCL: partial charge fitting - free QM package Message-Id: <-29600-051013191114-19095-mMhCc7zLGCfLZ0QczuOQMA###server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 13 Oct 2005 16:11:01 -0700 MIME-Version: 1.0 Sent to CCL by: Mark Thompson [mark.|.arguslab.com] > I am constructing drug molecules to dock into a receptor using > molecular mechanics forcefield representation of atoms. The drug > molecules were built in Sybyl and partial charges were first added > using the Gasteiger-Marsili charges by default. I then performed an > AM1 MOPAC calculation to derive Mulliken charges which were differed > to some extent. I do not currently have a program to perform higher > level ab initio calculations from which tto derive better charges. > > Where may I obtain a free QM program that performs ab initio > calculations with acceptable basis sets for small organic molecules > from which to derive MM partial charges? GAMESS is a good program. It's free. (http://www.msg.ameslab.gov/GAMESS/GAMESS.html) Mark ---------------------------- Mark Thompson mark|arguslab.com http://www.arguslab.com ---------------------------- From owner-chemistry@ccl.net Thu Oct 13 22:07:00 2005 From: "Dr Seth Olsen s.olsen1::uq.edu.au" To: CCL Subject: CCL: partial charge fitting - free QM package Message-Id: <-29601-051013214846-21898-B51bRfV6M1mjK1tKasKdzw**server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 14 Oct 2005 11:48:37 +1000 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1::uq.edu.au] NwChem also does charge fitting. I'm not sure about the details of the license - it may not be free for commercial use. For academic use it is, but there is an agreement to be signed. The details are online. I would check out Linux4chemistry or some other open-source software repository site. There are a few programs which should be able to do what you want, depending on the level of ab initio theory you require and whether or not the program needs to do the fitting itself (as opposed to just generating the density or potential). Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1 ~ uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms ----- Original Message ----- > From: "Mark Thompson mark]~[arguslab.com" Date: Friday, October 14, 2005 9:11 am Subject: CCL: partial charge fitting - free QM package > > Sent to CCL by: Mark Thompson [mark. ~ .arguslab.com] > > > I am constructing drug molecules to dock into a receptor using > > molecular mechanics forcefield representation of atoms. The drug > > molecules were built in Sybyl and partial charges were first > added > > using the Gasteiger-Marsili charges by default. I then performed > an > > AM1 MOPAC calculation to derive Mulliken charges which were > differed > > to some extent. I do not currently have a program to perform > higher > > level ab initio calculations from which tto derive better charges. > > > > Where may I obtain a free QM program that performs ab initio > > calculations with acceptable basis sets for small organic > molecules > > from which to derive MM partial charges? > > GAMESS is a good program. It's free. > (http://www.msg.ameslab.gov/GAMESS/GAMESS.html) > > Mark > ---------------------------- > Mark Thompson > mark*arguslab.com > http://www.arguslab.com > ---------------------------- > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the ~ sign. You can > also> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Thu Oct 13 22:42:01 2005 From: "janl[-]speakeasy.net" To: CCL Subject: CCL: GCG Excellence Student Travel Award Stipends for ACS Atlanta Meeting Message-Id: <-29602-051013220527-23252-aBQdCsXLxfYbbUO7dtoXLQ:+:server.ccl.net> X-Original-From: janl#speakeasy.net Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 14 Oct 2005 02:05:21 +0000 MIME-Version: 1.0 Sent to CCL by: janl()speakeasy.net The CCG Excellence Awards were created to stimulate graduate student participation in COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award, are North American graduate students in good standing who present work within the COMP program, either in oral or poster format. Winners receive $1,150, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session. Details: http://membership.acs.org/C/COMP/CCG/ccg.html Deadline for applying: Nov. 1, 2005 Posted for ACS Comp Division by Jan Labanowski