From owner-chemistry@ccl.net Mon Jun 2 01:49:00 2014 From: "A Reisi areisi_+_kashanu.ac.ir" To: CCL Subject: CCL:G: Error in pop=NCS calculation with Gaussian 09 Message-Id: <-50134-140602014312-10144-Rb45Aoz+evXrKcr/2+DBLA{=}server.ccl.net> X-Original-From: "A Reisi" Date: Mon, 2 Jun 2014 01:43:10 -0400 Sent to CCL by: "A Reisi" [areisi*_*kashanu.ac.ir] Hi I want to do this calculation in Gaussian: #nmr=giao b3lyp/6-311+g(d) pop=ncs for Corannulene (C20H10) with 18 Bq atoms. Calculation was done with "Normal termination of Gaussian 09 ...." at the end of the output file but in "NATURAL BOND ORBITAL ANALYSIS" section Was typed "A bond orbital with an occupancy of 2.12700 electrons was found!" I need to this section. Please help to me if It is possible. A. Reisi From owner-chemistry@ccl.net Mon Jun 2 03:12:00 2014 From: "Simon Cross simon-*-moldiscovery.com" To: CCL Subject: CCL: software for docking waters? Message-Id: <-50135-140602031103-13684-g9sKEnK9uqFRADQRa4d2bg*_*server.ccl.net> X-Original-From: Simon Cross Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 2 Jun 2014 09:10:52 +0200 Mime-Version: 1.0 (1.0) Sent to CCL by: Simon Cross [simon%a%moldiscovery.com] Hi Matt, you can take a look at our approach in FLAP for predicting water networks and their use in docking (WaterFLAP and FLAPdock). There are details on our website at moldiscovery [dot] com My best, Simon Sent from my iPhone On 30 May 2014, at 19:05, "Matt Challacombe matt.challacombe#,#gmail.com" wrote: > > Sent to CCL by: Matt Challacombe [matt.challacombe|gmail.com] > Hi CCL, > > From the posts of Bin Sun & Prof. Case, I see there are great softwares for molecular docking. I'm wondering about a related problem I haven't seen much about, namely the docking of large water nets, eg. in active sites, binding pockets etc. Beyond just "do MD" is there an exhaustive approach? Maybe some experimental code? > > Cheers, Matt Challacombehttp://www.ccl.net/chemistry/sub_unsub.shtml> > From owner-chemistry@ccl.net Mon Jun 2 08:00:00 2014 From: "Laidig, Bill laidig.wd(_)pg.com" To: CCL Subject: CCL: DFT14poll Message-Id: <-50136-140601204631-21199-G1enabkfcY1aW/o2GzE/SQ_+_server.ccl.net> X-Original-From: "Laidig, Bill" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Mon, 2 Jun 2014 00:45:27 +0000 MIME-Version: 1.0 Sent to CCL by: "Laidig, Bill" [laidig.wd=pg.com] I strongly disagree with this position. There are many scientifically valid reasons to know which functionals are most popular among theoretical and computational chemists (who, I am assuming, are the bulk of this mailing list). For example: 1. Even if a functional is clearly inferior to another, if it is used much more in real calculations then there may be several reasons to use the inferior function: a. It is likely more widely implemented meaning you have a wider choice of programs to use and ways to validate that the calculations were performed correctly. b. Wider use means that there is a larger statistical pool of data for assessing accuracy, etc. This is often much more important than using a marginally better method. We see this in the long-term popularity of methods such as HF/3-21G, and B3LYP/6-31G*. 2. Highly accurate, but arcane theoretical methods make communication of results difficult outside the expert community as the reader has little basis for assessing the quality of results. I learned this the hard way in my career in industry. Most users of computational chemistry want to know what small handful of methods can be applied broadly to large classes of problems. As experts, we are the group that is defining the next generation of standard methods so I find it very useful to know in what directions we are heading. Learning why we are using functionals can also let the developer of the "next big thing" know when their efforts to publicize and promote their methodology has fallen short and inspire them to better efforts in the future. Bill Laidig -----Original Message----- > From: owner-chemistry+laidig.wd==pg.com,ccl.net [mailto:owner-chemistry+laidig.wd==pg.com,ccl.net] On Behalf Of Robert Molt Jr r.molt.chemical.physics!=!gmail.com Sent: Sunday, June 01, 2014 3:07 PM To: Laidig, Bill Subject: CCL: DFT14poll Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics]_[gmail.com] Sirs and Madames: A "popularity contest" is anathema to science. The world should not weight the opinion of Rodney Bartlett and Robert Molt equally in coupled cluster theory. Perhaps we should take a poll on what people think the first spherical harmonic is? Or take a poll on whether Planck's constant is too small? Evidence and and logic drive science. -Robert Molt On 06/01/2014 12:26 PM, Víctor Luaña Cabal victor,fluor.quimica.uniovi.es wrote: > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal > [victor-.-fluor.quimica.uniovi.es] > On Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S h.rzepa:imperial.ac.uk wrote: >> Can I suggest that in future this poll be extended to indicate WHY any person indicates they LIKE a functional? As we all know, the choice of functional so often depends on what the property of interest is. >> >> I suggest initially a relatively short controlled list of properties, >> which can then be extended by “crowd sourcing”. Properties I have >> in mind might be eg >> >> 1. Reaction barriers >> 2. Normal mode analysis >> 3. Chiroptical properties >> 4. Hydrogen bonds >> 5. Excitation energies >> 6. Main group elements >> 7. Transition metals >> 8. Relativistic elements >> 9. NMR shieldings, NMR couplings >> 10. etc >> >> That way, we could find out eg the most liked functional for eg >> looking at hydrogen bonds. That would be enormously helpful to >> anyone looking to study eg hydrogen bonds. > Dear Prof. Rzepa, > > I have a deep respect for your work, that I use to love, but in this > case I dislike strongly the idea of deciding the use of a functional > by popularity. There are plenty of examples in which the most popular > route was not the best, just the easiest. It took decades, in many > cases, to turn back wrong but popular decisions. Two candidates should > be advised to create a safe road: the easiest AND the the best > founded. Notice that the most popular is not in my list. Popularity > can be obtained by well studied techniques that have nothing to do > with any real measurement of quality. > > As for your list of properties it is very useful and I will keep it > carefully. > > Best regards, > Dr. Víctor Luaña > > -- > \|/ > |^.^| > +---!OO--\_/--OO!------------------------------+---------------------- > +- > ! Dr.Víctor Luaña ! > ! Departamento de Química Física y Analítica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor*fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)http://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 Mon Jun 2 08:35:00 2014 From: "Jan Halborg Jensen jhjensen*_*chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: May issue Message-Id: <-50137-140602043734-16801-QmQDXrXaqrJcdlE9K+OPLw^-^server.ccl.net> X-Original-From: Jan Halborg Jensen Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_3960ACC4F7E1574EBB19AFC61B2389FDAFCDD8A7P1KITMBX03WC02u_" Date: Mon, 2 Jun 2014 08:37:15 +0000 MIME-Version: 1.0 Sent to CCL by: Jan Halborg Jensen [jhjensen+*+chem.ku.dk] --_000_3960ACC4F7E1574EBB19AFC61B2389FDAFCDD8A7P1KITMBX03WC02u_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable The May issue of Computational Chemistry Highlights is out. CCH is an overlay journal tha= t identifies the most important papers in computational and theoretical che= mistry published in the last 1-2 years. CCH is not affiliated with any publ= isher: it is a free resource run by scientists for scientists. You can read= more about it here. Table of content for this issue features contributions from CCH editors Ste= ven Bachrach and Jan Jensen: Phase Transition of [2,2]-Paracyclophane =96 An End to an Apparently Endles= s Story Monte Carlo Free Ligand Diffusion with Markov State Model Analysis and Abso= lute Binding Free Energy Calculations Polytwistane Quantification of Nonstatistical Dynamics in an Intramolecular Diels=96Alde= r Cyclization without Trajectory Computation. How Small Can a Catenane Be? Interested in more? There are many ways to subscribe to CCH updates. --_000_3960ACC4F7E1574EBB19AFC61B2389FDAFCDD8A7P1KITMBX03WC02u_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

The May issue of Computational Chemi= stry Highlights is out.


CCH is an ove= rlay journal that identifies the most important papers in computat= ional and theoretical chemistry published in the last 1-2 years. CCH is not= affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.


Table of content for this issue features contributions from CCH editors Ste= ven Bachrach and Jan Jensen:


Phase Transition of [2,2]-Paracyclophane =96 An End t= o an Apparently Endless Story






= --_000_3960ACC4F7E1574EBB19AFC61B2389FDAFCDD8A7P1KITMBX03WC02u_-- From owner-chemistry@ccl.net Mon Jun 2 09:10:00 2014 From: "N. Sukumar nagams-x-rpi.edu" To: CCL Subject: CCL: DFT14poll Message-Id: <-50138-140602074433-5214-z5fp0rAyPyyAlVnpmdIH/w[*]server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Mon, 02 Jun 2014 7:45:26 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams__rpi.edu] "A popularity contest is anathema to science... Evidence and and logic drive science." In principle, yes. But important hiring and promotion decisions are often based at least in part on citation statistics and impact factors. I see this popularity contest on DFT functionals as no more than a social media tool such as "what are your colleagues reading these days?" Attempts to bias the results by multiple or robotic voting are misguided, as are efforts to read more meaning into these "popularity" data. Information on WHY and for which applications specific functionals are most useful are valuable, as are statistics on the number of PAPERS (rather than the number of people) "liking" a functional, but these data are best left to serious reviews. N. Sukumar Professor of Chemistry Shiv Nadar University, India ---------------------------- "Pursue something so important that even if you fail, the world is better off with you having tried." -- Tim O'Reilly http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470769009.html ==============Original message text=============== On Sun, 01 Jun 2014 15:07:06 EDT "Robert Molt Jr r.molt.chemical.physics!=!gmail.com" wrote: Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics]_[gmail.com] Sirs and Madames: A "popularity contest" is anathema to science. The world should not weight the opinion of Rodney Bartlett and Robert Molt equally in coupled cluster theory. Perhaps we should take a poll on what people think the first spherical harmonic is? Or take a poll on whether Planck's constant is too small? Evidence and and logic drive science. -Robert Molt On 06/01/2014 12:26 PM, Víctor Luaña Cabal victor,fluor.quimica.uniovi.es wrote: > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor-.-fluor.quimica.uniovi.es] > On Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S h.rzepa:imperial.ac.uk wrote: >> Can I suggest that in future this poll be extended to indicate WHY any person indicates they LIKE a functional? As we all know, the choice of functional so often depends on what the property of interest is. >> >> I suggest initially a relatively short controlled list of properties, which can then be extended by “crowd sourcing”. Properties I have in mind might be eg >> >> 1. Reaction barriers >> 2. Normal mode analysis >> 3. Chiroptical properties >> 4. Hydrogen bonds >> 5. Excitation energies >> 6. Main group elements >> 7. Transition metals >> 8. Relativistic elements >> 9. NMR shieldings, NMR couplings >> 10. etc >> >> That way, we could find out eg the most liked functional for eg looking >> at hydrogen bonds. That would be enormously helpful to anyone looking >> to study eg hydrogen bonds. > Dear Prof. Rzepa, > > I have a deep respect for your work, that I use to love, but in this > case I dislike strongly the idea of deciding the use of a functional by > popularity. There are plenty of examples in which the most popular route > was not the best, just the easiest. It took decades, in many cases, to > turn back wrong but popular decisions. Two candidates should be advised > to create a safe road: the easiest AND the the best founded. Notice that > the most popular is not in my list. Popularity can be obtained by well > studied techniques that have nothing to do with any real measurement > of quality. > > As for your list of properties it is very useful and I will keep it > carefully. > > Best regards, > Dr. Víctor Luaña > > -- > \|/ > |^.^| > +---!OO--\_/--OO!------------------------------+----------------------- > ! Dr.Víctor Luaña ! > ! Departamento de Química Física y Analítica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor*fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Mon Jun 2 09:44:00 2014 From: "bonoit bonoit ablux13^_^gmail.com" To: CCL Subject: CCL: Critical energy using RRKM Message-Id: <-50139-140602090358-14049-XUQEXHVlfzNF6nv+aLCCkQ_-_server.ccl.net> X-Original-From: "bonoit bonoit" Date: Mon, 2 Jun 2014 09:03:57 -0400 Sent to CCL by: "bonoit bonoit" [ablux13#gmail.com] Dear CCLers, I would like to do some calculations of critical energy using RRKM theory. The given formulae for such calculation is as: E= Eclassical + sum (...) My question is about this E classical, what does it represent and how would I calculate it? Cordially, Bonoit From owner-chemistry@ccl.net Mon Jun 2 10:20:01 2014 From: "tuxiong qianchengshen^gmail.com" To: CCL Subject: CCL:G: Gaussian 09 "Open-new-file" Error Message-Id: <-50140-140602095543-9475-5evXSggXnibZB+3WyvNp+Q ~ server.ccl.net> X-Original-From: tuxiong Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 2 Jun 2014 21:55:25 +0800 Mime-Version: 1.0 (1.0) Sent to CCL by: tuxiong [qianchengshen:gmail.com] Dear CCLers, I run same Gaussian gif file and same LSF submission script on the same node of the computer clusters, but some (about 30%) of my jobs terminated with "open-new-file" in the bottom line of the log file , and the others finished. Dose anyone know why or could provide any hints? Thank you very much. Shen > From my iphone From owner-chemistry@ccl.net Mon Jun 2 12:43:00 2014 From: "Abrash, Samuel sabrash!^!richmond.edu" To: CCL Subject: CCL: DFT14poll Message-Id: <-50141-140602101739-29041-c73jJOZr/4TplK6BT+iflQ^^^server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Mon, 2 Jun 2014 14:17:30 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash..richmond.edu] I think people are taking the words "popularity contest" too seriously. It's just a poll to find out what members of this listserve, who are mostly computational chemistry professionals, are using. I agree that the absence of "why" makes this somewhat less useful. However, I think it's useful because if I see a functional that I don't know about used widely, I'm going to investigate it. (Note not blindly use it, but investigate it.) Still the why is a useful bit of information. For example, I use M062X for many of my calculations now, and if asked why, I'd say "because reviewers insisted that it's better for complexes than PBEPBE even though my results come out the same with either functional, and I wanted my paper published." Best, Sam -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu#ccl.net [mailto:owner-chemistry+sabrash==richmond.edu#ccl.net] On Behalf Of Laidig, Bill laidig.wd(_)pg.com Sent: Sunday, June 01, 2014 8:45 PM To: Abrash, Samuel Subject: CCL: DFT14poll Sent to CCL by: "Laidig, Bill" [laidig.wd=pg.com] I strongly disagree with this position. There are many scientifically valid reasons to know which functionals are most popular among theoretical and computational chemists (who, I am assuming, are the bulk of this mailing list). For example: 1. Even if a functional is clearly inferior to another, if it is used much more in real calculations then there may be several reasons to use the inferior function: a. It is likely more widely implemented meaning you have a wider choice of programs to use and ways to validate that the calculations were performed correctly. b. Wider use means that there is a larger statistical pool of data for assessing accuracy, etc. This is often much more important than using a marginally better method. We see this in the long-term popularity of methods such as HF/3-21G, and B3LYP/6-31G*. 2. Highly accurate, but arcane theoretical methods make communication of results difficult outside the expert community as the reader has little basis for assessing the quality of results. I learned this the hard way in my career in industry. Most users of computational chemistry want to know what small handful of methods can be applied broadly to large classes of problems. As experts, we are the group that is defining the next generation of standard methods so I find it very useful to know in what directions we are heading. Learning why we are using functionals can also let the developer of the "next big thing" know when their efforts to publicize and promote their methodology has fallen short and inspire them to better efforts in the future. Bill Laidig -----Original Message----- > From: owner-chemistry+laidig.wd==pg.com^ccl.net > [mailto:owner-chemistry+laidig.wd==pg.com^ccl.net] On Behalf Of Robert > Molt Jr r.molt.chemical.physics!=!gmail.com Sent: Sunday, June 01, 2014 3:07 PM To: Laidig, Bill Subject: CCL: DFT14poll Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics]_[gmail.com] Sirs and Madames: A "popularity contest" is anathema to science. The world should not weight the opinion of Rodney Bartlett and Robert Molt equally in coupled cluster theory. Perhaps we should take a poll on what people think the first spherical harmonic is? Or take a poll on whether Planck's constant is too small? Evidence and and logic drive science. -Robert Molt On 06/01/2014 12:26 PM, Víctor Luaña Cabal victor,fluor.quimica.uniovi.es wrote: > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal > [victor-.-fluor.quimica.uniovi.es] > On Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S h.rzepa:imperial.ac.uk wrote: >> Can I suggest that in future this poll be extended to indicate WHY any person indicates they LIKE a functional? As we all know, the choice of functional so often depends on what the property of interest is. >> >> I suggest initially a relatively short controlled list of properties, >> which can then be extended by “crowd sourcing”. Properties I have >> in mind might be eg >> >> 1. Reaction barriers >> 2. Normal mode analysis >> 3. Chiroptical properties >> 4. Hydrogen bonds >> 5. Excitation energies >> 6. Main group elements >> 7. Transition metals >> 8. Relativistic elements >> 9. NMR shieldings, NMR couplings >> 10. etc >> >> That way, we could find out eg the most liked functional for eg >> looking at hydrogen bonds. That would be enormously helpful to >> anyone looking to study eg hydrogen bonds. > Dear Prof. Rzepa, > > I have a deep respect for your work, that I use to love, but in this > case I dislike strongly the idea of deciding the use of a functional > by popularity. There are plenty of examples in which the most popular > route was not the best, just the easiest. It took decades, in many > cases, to turn back wrong but popular decisions. Two candidates should > be advised to create a safe road: the easiest AND the the best > founded. Notice that the most popular is not in my list. Popularity > can be obtained by well studied techniques that have nothing to do > with any real measurement of quality. > > As for your list of properties it is very useful and I will keep it > carefully. > > Best regards, > Dr. Víctor Luaña > > -- > \|/ > |^.^| > +---!OO--\_/--OO!------------------------------+---------------------- > +- > ! Dr.Víctor Luaña ! > ! Departamento de Química Física y Analítica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor*fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being > reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl > .net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://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 Mon Jun 2 13:18:00 2014 From: "Brian Skinn bskinn_-_alum.mit.edu" To: CCL Subject: CCL: DFT14poll Message-Id: <-50142-140602103505-13623-z2235HnJG1SbGN5xCH+Lrw**server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=001a11c244486efb7a04fadb4c84 Date: Mon, 2 Jun 2014 10:34:33 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [bskinn-*-alum.mit.edu] --001a11c244486efb7a04fadb4c84 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable "Information on WHY and for which applications specific functionals are most useful are valuable, as are statistics on the number of PAPERS (rather than the number of people) "liking" a functional, but these data are best left to serious reviews." Indeed, one could conceive of a number of review papers growing out of a comparison between the results of this survey ("What do researchers believe are the strengths of various functional?") and benchmark studies ("How do various functionals actually perform in their popularly believed areas of strength?") Kruse, Goerigk & Grimme (2012) [doi:10.1021/jo302156p] comes to mind as a recent example. Such reviews would dabble a bit in the sociology of the matter, but could perhaps still be helpful in guiding the science toward increased rigor. Brian Skinn PhD, Chemical Engineering, MIT On Mon, Jun 2, 2014 at 7:45 AM, N. Sukumar nagams-x-rpi.edu < owner-chemistry-*-ccl.net> wrote: > > Sent to CCL by: "N. Sukumar" [nagams__rpi.edu] > "A popularity contest is anathema to science... Evidence and and logic > drive science." > > In principle, yes. But important hiring and promotion decisions are often > based at least in part on citation statistics and impact factors. > > I see this popularity contest on DFT functionals as no more than a social > media tool such as "what are your colleagues reading these days?" > Attempts to bias the results by multiple or robotic voting are misguided, > as are efforts to read more meaning into these "popularity" data. > > Information on WHY and for which applications specific functionals are > most useful are valuable, as are statistics on the number of PAPERS > (rather than the number of people) "liking" a functional, but these data > are best left to serious reviews. > > N. Sukumar > Professor of Chemistry > Shiv Nadar University, India > ---------------------------- > "Pursue something so important that even if you fail, the world is better > off with you having tried." -- Tim O'Reilly > http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470769009.html > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3DOriginal message text=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > On Sun, 01 Jun 2014 15:07:06 EDT "Robert Molt Jr > r.molt.chemical.physics!=3D!gmail.com" wrote: > > > Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics]_[gmail.com] > Sirs and Madames: > > A "popularity contest" is anathema to science. The world should not > weight the opinion of Rodney Bartlett and Robert Molt equally in coupled > cluster theory. > > Perhaps we should take a poll on what people think the first spherical > harmonic is? Or take a poll on whether Planck's constant is too small? > > Evidence and and logic drive science. > > -Robert Molt > > On 06/01/2014 12:26 PM, V=C3=ADctor Lua=C3=B1a Cabal > victor,fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal > [victor-.-fluor.quimica.uniovi.es] > > On Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S > h.rzepa:imperial.ac.uk wrote: > >> Can I suggest that in future this poll be extended to indicate WHY > any person indicates they LIKE a functional? As we all know, the choice > of functional so often depends on what the property of interest is. > >> > >> I suggest initially a relatively short controlled list of properties, > which can then be extended by =E2=80=9Ccrowd sourcing=E2=80=9D. Properti= es I have > in mind might be eg > >> > >> 1. Reaction barriers > >> 2. Normal mode analysis > >> 3. Chiroptical properties > >> 4. Hydrogen bonds > >> 5. Excitation energies > >> 6. Main group elements > >> 7. Transition metals > >> 8. Relativistic elements > >> 9. NMR shieldings, NMR couplings > >> 10. etc > >> > >> That way, we could find out eg the most liked functional for eg lookin= g > >> at hydrogen bonds. That would be enormously helpful to anyone looking > >> to study eg hydrogen bonds. > > Dear Prof. Rzepa, > > > > I have a deep respect for your work, that I use to love, but in this > > case I dislike strongly the idea of deciding the use of a functional by > > popularity. There are plenty of examples in which the most popular rout= e > > was not the best, just the easiest. It took decades, in many cases, to > > turn back wrong but popular decisions. Two candidates should be advised > > to create a safe road: the easiest AND the the best founded. Notice tha= t > > the most popular is not in my list. Popularity can be obtained by well > > studied techniques that have nothing to do with any real measurement > > of quality. > > > > As for your list of properties it is very useful and I will keep it > > carefully. > > > > Best regards, > > Dr. V=C3=ADctor Lua=C3=B1a > > > > -- > > \|/ > > |^.^| > > +---!OO--\_/--OO!------------------------------+----------------------- > > ! Dr.V=C3=ADctor Lua=C3=B1a ! > > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > > ! e-mail: victor*fluor.quimica.uniovi.es ! > > ! phone: +34-985-103491 fax: +34-985-103125 ! > > +----------------------------------------------+ > > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)http://www.ccl.net/chemist= ry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3DEnd > of original message text=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a11c244486efb7a04fadb4c84 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
"Information on WHY and for which applications specific functionals = are
most useful are valuab= le, as are statistics on the number of PAPERS
(rather than th= e number of people) "liking" a functional, but these data<= br style=3D"font-family:arial,sans-serif;font-size:13px">are best left to serious reviews.= "

Indeed, = one could conceive of a number of review papers growing out of a comparison= between the results of this survey ("What do researchers believe are = the strengths of various functional?") and benchmark studies ("Ho= w do various functionals actually perform in their popularly believed areas= of strength?") =C2=A0Kruse, Goerigk & Grimme (2012)=C2=A0[doi:10.1021/jo302156p]=C2=A0comes to m= ind as a recent example. =C2=A0Such reviews would dabble a bit in the socio= logy of the matter, but could perhaps still be helpful in guiding the scien= ce toward increased rigor.


Brian Skinn
PhD, Chemi= cal Engineering, MIT





On Mon, Jun 2, 2014 at 7:45 AM, N. Sukumar nagams-x-rpi.edu <owner-chemistry-*-ccl.net&g= t; wrote:

Sent to CCL by: "N. Sukumar" [nagams__rpi.edu]
"A popularity contest is anathema to science... Evidence and and logic=
drive science."

In principle, yes. But important hiring and promotion decisions are often based at least in part on citation statistics and impact factors.

I see this popularity contest on DFT functionals as no more than a social media tool such as "what are your colleagues reading these days?"=
Attempts to bias the results by multiple or robotic voting are misguided, as are efforts to read more meaning into these "popularity" data.=

Information on WHY and for which applications specific functionals are
most useful are valuable, as are statistics on the number of PAPERS
(rather than the number of people) "liking" a functional, but the= se data
are best left to serious reviews.

N. Sukumar
Professor of Chemistry
Shiv Nadar University, India
----------------------------
"Pursue something so important that even if you fail, the world is bet= ter
off with you having tried." -- Tim O'Reilly
http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470= 769009.html
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3DOriginal message text=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
On Sun, 01 Jun 2014 15:07:06 EDT "Robert Molt J= r
r.molt.chemical.physics!=3D!= gmail.com" wrote:


Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics]_[gmail.com]
Sirs and Madames:

A "popularity contest" is anathema to science. =C2=A0The world sh= ould not
weight the opinion of Rodney Bartlett and Robert Molt equally in coupled cluster theory.

Perhaps we should take a poll on what people think the first spherical
harmonic is? =C2=A0Or take a poll on whether Planck's constant is too s= mall?

Evidence and and logic drive science.

-Robert Molt

On 06/01/2014 12:26 PM, V=C3=ADctor Lua=C3=B1a Cabal
victor,fluor.q= uimica.uniovi.es wrote:
> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal
[victor-.-fluo= r.quimica.uniovi.es]
> On Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S
h.rzepa:imperial.ac.uk<= /a> wrote:
>> Can =C2=A0I suggest that in future this poll be extended to indica= te WHY
any person indicates they =C2=A0LIKE =C2=A0a functional? As we all know, th= e choice
of functional so often depends on what the property of interest is.
>>
>> I suggest initially a relatively short controlled list of properti= es,
which can then be extended by =C2=A0=E2=80=9Ccrowd sourcing=E2=80=9D. Prope= rties =C2=A0I have
in mind might be eg
>>
>> 1. Reaction barriers
>> 2. Normal mode analysis
>> 3. Chiroptical properties
>> 4. Hydrogen bonds
>> 5. Excitation energies
>> 6. Main group elements
>> 7. Transition metals
>> 8. Relativistic elements
>> 9. NMR shieldings, NMR couplings
>> 10. etc
>>
>> That way, we could find out eg the most liked functional for eg lo= oking
>> at hydrogen bonds. =C2=A0That would be enormously helpful to anyon= e looking
>> to study eg hydrogen bonds.
> Dear Prof. Rzepa,
>
> I have a deep respect for your work, that I use to love, but in this > case I dislike strongly the idea of deciding the use of a functional b= y
> popularity. There are plenty of examples in which the most popular rou= te
> was not the best, just the easiest. It took decades, in many cases, to=
> turn back wrong but popular decisions. Two candidates should be advise= d
> to create a safe road: the easiest AND the the best founded. Notice th= at
> the most popular is not in my list. Popularity can be obtained by well=
> studied techniques that have nothing to do with any real measurement > of quality.
>
> As for your list of properties it is very useful and I will keep it > carefully.
>
> Best regards,
> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua= =C3=B1a
>
> --
> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 \|/
> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0|^.^|
> +---!OO--\_/--OO!------------------------------+----------= -------------
> ! =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Dr.V=C3=ADc= tor Lua=C3=B1a =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 !
> ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica =C2=A0 ! > ! Universidad de Oviedo, 33006-Oviedo, Spain =C2=A0 !
> ! e-mail: =C2=A0 victor*fluor.quimica.uniovi.es =C2=A0 =C2=A0 !
> ! phone: +34-9= 85-103491 =C2=A0fax: +34-985-103125 =C2=A0 !
> +----------------------------------------------+
> =C2=A0 GroupPage : http://azufre.quimica.uniovi.es/ =C2=A0(being reworke= d)http://www.ccl.net/cgi-bin/ccl/sen= d_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net= /spammers.txt=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3DEnd of original message t= ext=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D



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--001a11c244486efb7a04fadb4c84-- From owner-chemistry@ccl.net Mon Jun 2 13:53:00 2014 From: "Stella Kritikou skritikou1(-)sheffield.ac.uk" To: CCL Subject: CCL:G: Gaussian 09 "Open-new-file" Error Message-Id: <-50143-140602114338-2411-uz4sfQ+f6zU5Cv+8X5+xgg() server.ccl.net> X-Original-From: Stella Kritikou Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 02 Jun 2014 16:43:29 +0100 MIME-Version: 1.0 Sent to CCL by: Stella Kritikou [skritikou1_._sheffield.ac.uk] On 6/2/14, 2:55 PM, tuxiong qianchengshen^gmail.com wrote: > Sent to CCL by: tuxiong [qianchengshen:gmail.com] > Dear CCLers, > I run same Gaussian gif file and same LSF submission script on the same node of the computer clusters, but some (about 30%) of my jobs terminated with "open-new-file" in the bottom line of the log file , and the others finished. Dose anyone know why or could provide any hints? > Thank you very much. > > Shen > >> From my iphone> > Make sure that the line pointing at your checkpoint file actually ends in .chp and not .com! I've encountered this error in many cases when I forgot to change the extension! -- Stella Kritikou PhD student in Theoretical Chemistry Deparment of Chemistry, Room G5 University of Sheffield S3 7HF, UK From owner-chemistry@ccl.net Mon Jun 2 14:28:00 2014 From: "Chang, Christopher Christopher.Chang_._nrel.gov" To: CCL Subject: CCL: DFT14poll Message-Id: <-50144-140602121530-4730-LJgLj/7dwXr1ZdmbYo8ROw:server.ccl.net> X-Original-From: "Chang, Christopher" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Mon, 2 Jun 2014 10:15:19 -0600 MIME-Version: 1.0 Sent to CCL by: "Chang, Christopher" [Christopher.Chang^nrel.gov] Appeals to authority are also dangerous. Why should we not weight Drs. Molt's and Bartlett's opinions equally? If the opinions are grounded in evidence and logic, then the opinion is only a convenient proxy for that deeper and more meaningful evidence and logic. The value of opinion polls is highly dependent on their intended usage. The first poll example on spherical harmonics would be perfectly respectable as an entrance/exit contrast poll for students. The second is probably run in the theoretical physics community among people whose lives revolve around the precision and accuracy of Planck's constant. Nonetheless, I do hope that the poll publication will include some language about intent (and conversely, poor uses of such information). I really like Dr. Rzepa's idea of categorization by a controlled vocabulary of physical chemical phenomena. The results could serve as a nice starting point for answering questions re: DF vs. property I see on the list. - CHC -----Original Message----- > From: owner-chemistry+christopher.chang==nrel.gov-x-ccl.net [mailto:owner-chemistry+christopher.chang==nrel.gov-x-ccl.net] On Behalf Of Robert Molt Jr r.molt.chemical.physics!=!gmail.com Sent: Sunday, June 01, 2014 1:07 PM To: Chang, Christopher Subject: CCL: DFT14poll Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics]_[gmail.com] Sirs and Madames: A "popularity contest" is anathema to science. The world should not weight the opinion of Rodney Bartlett and Robert Molt equally in coupled cluster theory. Perhaps we should take a poll on what people think the first spherical harmonic is? Or take a poll on whether Planck's constant is too small? Evidence and and logic drive science. -Robert Molt On 06/01/2014 12:26 PM, Víctor Luaña Cabal victor,fluor.quimica.uniovi.es wrote: > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal > [victor-.-fluor.quimica.uniovi.es] > On Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S h.rzepa:imperial.ac.uk wrote: >> Can I suggest that in future this poll be extended to indicate WHY any person indicates they LIKE a functional? As we all know, the choice of functional so often depends on what the property of interest is. >> >> I suggest initially a relatively short controlled list of properties, >> which can then be extended by “crowd sourcing”. Properties I have >> in mind might be eg >> >> 1. Reaction barriers >> 2. Normal mode analysis >> 3. Chiroptical properties >> 4. Hydrogen bonds >> 5. Excitation energies >> 6. Main group elements >> 7. Transition metals >> 8. Relativistic elements >> 9. NMR shieldings, NMR couplings >> 10. etc >> >> That way, we could find out eg the most liked functional for eg >> looking at hydrogen bonds. That would be enormously helpful to >> anyone looking to study eg hydrogen bonds. > Dear Prof. Rzepa, > > I have a deep respect for your work, that I use to love, but in this > case I dislike strongly the idea of deciding the use of a functional > by popularity. There are plenty of examples in which the most popular > route was not the best, just the easiest. It took decades, in many > cases, to turn back wrong but popular decisions. Two candidates should > be advised to create a safe road: the easiest AND the the best > founded. Notice that the most popular is not in my list. Popularity > can be obtained by well studied techniques that have nothing to do > with any real measurement of quality. > > As for your list of properties it is very useful and I will keep it > carefully. > > Best regards, > Dr. Víctor Luaña > > -- > \|/ > |^.^| > +---!OO--\_/--OO!------------------------------+---------------------- > +- > ! Dr.Víctor Luaña ! > ! Departamento de Química Física y Analítica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor*fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)http://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 Mon Jun 2 15:12:00 2014 From: "Haya Kornweitz hayak_-_ariel.ac.il" To: CCL Subject: CCL: Protein and Solvent Effects Message-Id: <-50145-140602150933-22571-8es0XnHrSoX8juc+EmKsdA]~[server.ccl.net> X-Original-From: "Haya Kornweitz" Date: Mon, 2 Jun 2014 15:09:32 -0400 Sent to CCL by: "Haya Kornweitz" [hayak#%#ariel.ac.il] Dear CCLs I am interested in DFT calculation of the active site of an enzyme (SOD) using g09. Is there a recommended procedure to take into account Protein and Solvent Effects? Are the PCM models relevants? Please let me know how you suggest to deal with this matter. Thanks Haya From owner-chemistry@ccl.net Mon Jun 2 15:47:00 2014 From: "Marcel Swart marcel.swart a icrea.cat" To: CCL Subject: CCL: DFT14poll Message-Id: <-50146-140602150351-18231-zVUuSLa9REs/yTi0LdfGbA * server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary="Apple-Mail=_C66F5E20-E6F0-4767-8614-F88E97D43AF7" Date: Mon, 2 Jun 2014 21:03:31 +0200 Mime-Version: 1.0 (Mac OS X Mail 7.3 \(1878.2\)) Sent to CCL by: Marcel Swart [marcel.swart_-_icrea.cat] --Apple-Mail=_C66F5E20-E6F0-4767-8614-F88E97D43AF7 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Dear all, We as organizers of the DFT-poll would like to bring forward (again) our = motivations to hold the DFT-popularity poll. We would not like the scientific community to = misinterpret the aims, nor the benefits of the results of the poll. As Victor Lua=F1a pointed = out, it can take a long time to make people aware of strong points and weaknesses of currently = available density functionals, and one of the advantages of the DFT-poll is to raise = awareness about new developments in DFT.=20 For example, one comment we have received over the past few years: =93I have never even heard of PBE0, how come it is one of the most = popular functionals ?=94 The aims of the poll are:=20 (i) to probe the =93preference of the community=94, i.e., setting up a = ranking of preferred DFT methods; and=20 (ii) provide a compilation of the =93de facto quality=94 that this = implies for the =93average DFT computation=94. We feel that the results do provide some insight in current preferences. = And interestingly , these preferences=20 do not always match with the best choice in terms of best agreement with = accurate reference data. The suggestion by Henry Rzepa to add the property of interest for the = preference indeed would give=20 additional insights, which would be very valuable to the community at = large. In summary, we are simply monitoring what happens in the field of DFT = and comment on how the choice=20 of the community differs from (or agrees with) reliable reference data. = In that way, we do exactly what should be done,=20 namely "drive science through evidence and logic" or may be even "drive = science back to evidence and logic=94=20 (because, against all basic principles of science, the community often = just follows blindly a fashion). Marcel Swart Matthias Bickelhaupt Miquel Duran PS. In the news-items from 2010-2012 we also included the number of = citations according to Web-Of-Science for all functionals involved; for some reason this was = not updated in 2013, but will be done again for the 2014 news-item On 01 Jun 2014, at 21:07, Robert Molt Jr = r.molt.chemical.physics!=3D!gmail.com wrote: >=20 > Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics]_[gmail.com] > Sirs and Madames: >=20 > A "popularity contest" is anathema to science. The world should not = weight the opinion of Rodney Bartlett and Robert Molt equally in coupled = cluster theory. >=20 > Perhaps we should take a poll on what people think the first spherical = harmonic is? Or take a poll on whether Planck's constant is too small? >=20 > Evidence and and logic drive science. >=20 > -Robert Molt >=20 > On 06/01/2014 12:26 PM, V=EDctor Lua=F1a Cabal = victor,fluor.quimica.uniovi.es wrote: >> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal = [victor-.-fluor.quimica.uniovi.es] >> On Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S = h.rzepa:imperial.ac.uk wrote: >>> Can I suggest that in future this poll be extended to indicate WHY = any person indicates they LIKE a functional? As we all know, the = choice of functional so often depends on what the property of interest = is. >>>=20 >>> I suggest initially a relatively short controlled list of = properties, which can then be extended by =93crowd sourcing=94. = Properties I have in mind might be eg >>>=20 >>> 1. Reaction barriers >>> 2. Normal mode analysis >>> 3. Chiroptical properties >>> 4. Hydrogen bonds >>> 5. Excitation energies >>> 6. Main group elements >>> 7. Transition metals >>> 8. Relativistic elements >>> 9. NMR shieldings, NMR couplings >>> 10. etc >>>=20 >>> That way, we could find out eg the most liked functional for eg = looking >>> at hydrogen bonds. That would be enormously helpful to anyone = looking >>> to study eg hydrogen bonds. >> Dear Prof. Rzepa, >>=20 >> I have a deep respect for your work, that I use to love, but in this >> case I dislike strongly the idea of deciding the use of a functional = by >> popularity. There are plenty of examples in which the most popular = route >> was not the best, just the easiest. It took decades, in many cases, = to >> turn back wrong but popular decisions. Two candidates should be = advised >> to create a safe road: the easiest AND the the best founded. Notice = that >> the most popular is not in my list. Popularity can be obtained by = well >> studied techniques that have nothing to do with any real measurement >> of quality. >>=20 >> As for your list of properties it is very useful and I will keep it >> carefully. >>=20 >> Best regards, >> Dr. V=EDctor Lua=F1a >>=20 >> -- >> \|/ >> |^.^| >> = +---!OO--\_/--OO!------------------------------+----------------------- >> ! Dr.V=EDctor Lua=F1a ! >> ! Departamento de Qu=EDmica F=EDsica y Anal=EDtica ! >> ! Universidad de Oviedo, 33006-Oviedo, Spain ! >> ! e-mail: victor*fluor.quimica.uniovi.es ! >> ! phone: +34-985-103491 fax: +34-985-103125 ! >> +----------------------------------------------+ >> GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)> >>=20 >=20 >=20 >=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 = change>=20>=20>=20=>=20>=20Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 =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 Prof. Dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional i Cat=E0lisi Universitat de Girona Facultat de Ci=E8ncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart#icrea.cat marcel.swart#udg.edu web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =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 --Apple-Mail=_C66F5E20-E6F0-4767-8614-F88E97D43AF7 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252 Dear all,

We as = organizers of the DFT-poll would like to bring forward (again) our = motivations to hold
the = DFT-popularity poll. We would not like the scientific community to = misinterpret the aims,
nor the benefits of the results of the poll. As Victor = Lua=F1a pointed out, it can take a long time
to make people aware of strong = points and weaknesses of currently available = density
functionals, and = one of the advantages of the DFT-poll is to raise awareness about = new
developments in = DFT. 
For example, = one comment we have received over the past few years:
=93I have never even heard of = PBE0, how come it is one of the most popular functionals ?=94

The aims of the poll are: 
(i) to probe the =93preference = of the community=94, i.e., setting up a ranking of preferred = DFT methods; and 
(ii) provide a compilation of the = =93de facto quality=94 that this implies for the =93average= DFT computation=94.
We = feel that the results do provide some insight in current = preferences. And interestingly , these preferences 
do not always match with = the best choice in terms of best agreement with = accurate reference data.
The suggestion by Henry Rzepa to add the property of = interest for  the preference indeed would give 
additional insights, which would = be very valuable to the community at large.

In summary, we are simply monitoring what happens in = the field of DFT and comment on how the choice 
of the community differs from (or = agrees with) reliable reference data. In that way, we do exactly what = should be done, 
namely "drive science through evidence and logic" or may = be even "drive science back to evidence and logic=94 
(because, against all basic = principles of science, the community often just follows blindly = a fashion).

Marcel Swart
Matthias Bickelhaupt
Miquel = Duran

PS.
In the = news-items from 2010-2012 we also included the number of citations = according
to Web-Of-Science for all functionals involved; for = some reason this was not updated
in 2013, but will be done = again for the 2014 news-item

On 01 Jun = 2014, at 21:07, Robert Molt Jr r.molt.chemical.physics!=3D!gmail.com <owner-chemistry#ccl.net> = wrote:


Sent to CCL by: Robert Molt Jr = [r.molt.chemical.physics]_[gmail.com]
Sirs and Madames:

A = "popularity contest" is anathema to science.  The world should not = weight the opinion of Rodney Bartlett and Robert Molt equally in coupled = cluster theory.

Perhaps we should take a poll on what people = think the first spherical harmonic is?  Or take a poll on whether = Planck's constant is too small?

Evidence and and logic drive = science.

-Robert Molt

On 06/01/2014 12:26 PM, V=EDctor = Lua=F1a Cabal victor,fluor.quimica.uniovi.es = wrote:
Sent to CCL by: = =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor-.-fluor.quimica.uniovi.es]
On= Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S = h.rzepa:imperial.ac.uk wrote:
Can  I = suggest that in future this poll be extended to indicate WHY any person = indicates they  LIKE  a functional? As we all know, the choice = of functional so often depends on what the property of interest = is.

I suggest initially a relatively short controlled list of = properties, which can then be extended by  =93crowd sourcing=94. = Properties  I have in mind might be eg

1. Reaction = barriers
2. Normal mode analysis
3. Chiroptical properties
4. = Hydrogen bonds
5. Excitation energies
6. Main group elements
7. = Transition metals
8. Relativistic elements
9. NMR shieldings, NMR = couplings
10. etc

That way, we could find out eg the most = liked functional for eg looking
at hydrogen bonds.  That would = be enormously helpful to anyone looking
to study eg hydrogen = bonds.
Dear Prof. Rzepa,

I have a deep respect = for your work, that I use to love, but in this
case I dislike = strongly the idea of deciding the use of a functional by
popularity. = There are plenty of examples in which the most popular route
was not = the best, just the easiest. It took decades, in many cases, to
turn = back wrong but popular decisions. Two candidates should be advised
to = create a safe road: the easiest AND the the best founded. Notice = that
the most popular is not in my list. Popularity can be obtained = by well
studied techniques that have nothing to do with any real = measurement
of quality.

As for your list of properties it is = very useful and I will keep it
carefully.

Best regards,
=             &n= bsp;Dr. V=EDctor Lua=F1a

--
=          \|/
=         |^.^|
+---!OO--\_/--OO!= ------------------------------+-----------------------
! =            Dr.V=EDc= tor Lua=F1a =             &n= bsp;     !
! Departamento de Qu=EDmica = F=EDsica y Anal=EDtica   !
! Universidad de Oviedo, = 33006-Oviedo, Spain   !
! e-mail:   victor*fluor.quimica.uniovi.es =     !
! phone: +34-985-103491  fax: = +34-985-103125 =   !
+----------------------------------------------+
=  GroupPage : http://azufre.quimica.uniovi.es/=  (being reworked)>




-=3D = This is automatically added to each message by the mailing script = =3D-
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= --Apple-Mail=_C66F5E20-E6F0-4767-8614-F88E97D43AF7-- From owner-chemistry@ccl.net Mon Jun 2 18:06:00 2014 From: "Steven Bachrach sbachrac]|[trinity.edu" To: CCL Subject: CCL: DFT14poll Message-Id: <-50147-140602163835-18985-S20erQOBbBT8bfgjsMDaWA^^^server.ccl.net> X-Original-From: Steven Bachrach Content-Type: multipart/alternative; boundary=047d7b6dc67aad7c3604fae0607d Date: Mon, 2 Jun 2014 15:38:28 -0500 MIME-Version: 1.0 Sent to CCL by: Steven Bachrach [sbachrac(a)trinity.edu] --047d7b6dc67aad7c3604fae0607d Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I also think the poll has value in discerning trends, especially new funtionals to appear on the list and ones that have fallen down or off. Steven On Mon, Jun 2, 2014 at 9:17 AM, Abrash, Samuel sabrash!^!richmond.edu < owner-chemistry]=[ccl.net> wrote: > > Sent to CCL by: "Abrash, Samuel" [sabrash..richmond.edu] > I think people are taking the words "popularity contest" too seriously. > It's just a poll to find out what members of this listserve, who are > mostly computational chemistry professionals, are using. I agree that th= e > absence of "why" makes this somewhat less useful. However, I think it's > useful because if I see a functional that I don't know about used widely, > I'm going to investigate it. (Note not blindly use it, but investigate > it.) Still the why is a useful bit of information. For example, I use > M062X for many of my calculations now, and if asked why, I'd say "because > reviewers insisted that it's better for complexes than PBEPBE even though > my results come out the same with either functional, and I wanted my pape= r > published." > > Best, > Sam > > -----Original Message----- > > From: owner-chemistry+sabrash=3D=3Drichmond.edu . ccl.net [mailto: > owner-chemistry+sabrash=3D=3Drichmond.edu . ccl.net] On Behalf Of Laidig, > Bill laidig.wd(_)pg.com > Sent: Sunday, June 01, 2014 8:45 PM > To: Abrash, Samuel > Subject: CCL: DFT14poll > > > Sent to CCL by: "Laidig, Bill" [laidig.wd=3Dpg.com] I strongly disagree > with this position. There are many scientifically valid reasons to know > which functionals are most popular among theoretical and computational > chemists (who, I am assuming, are the bulk of this mailing list). For > example: > > 1. Even if a functional is clearly inferior to another, if it is used muc= h > more in real calculations then there may be several reasons to use the > inferior function: > a. It is likely more widely implemented meaning you have a wider > choice of programs > to use and ways to validate that the calculations were performe= d > correctly. > b. Wider use means that there is a larger statistical pool of data > for assessing accuracy, > etc. This is often much more important than using a marginally > better method. We > see this in the long-term popularity of methods such as HF/3-21G= , > and B3LYP/6-31G*. > 2. Highly accurate, but arcane theoretical methods make communication of > results difficult outside the expert community as the reader has little > basis for assessing the quality of results. I learned this the hard way = in > my career in industry. > > Most users of computational chemistry want to know what small handful of > methods can be applied broadly to large classes of problems. As experts, > we are the group that is defining the next generation of standard methods > so I find it very useful to know in what directions we are heading. > Learning why we are using functionals can also let the developer of the > "next big thing" know when their efforts to publicize and promote their > methodology has fallen short and inspire them to better efforts in the > future. > > Bill Laidig > > -----Original Message----- > > From: owner-chemistry+laidig.wd=3D=3Dpg.com^ccl.net > > [mailto:owner-chemistry+laidig.wd=3D=3Dpg.com^ccl.net] On Behalf Of Rob= ert > > Molt Jr r.molt.chemical.physics!=3D!gmail.com > Sent: Sunday, June 01, 2014 3:07 PM > To: Laidig, Bill > Subject: CCL: DFT14poll > > > Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics]_[gmail.com] > Sirs and Madames: > > A "popularity contest" is anathema to science. The world should not > weight the opinion of Rodney Bartlett and Robert Molt equally in coupled > cluster theory. > > Perhaps we should take a poll on what people think the first spherical > harmonic is? Or take a poll on whether Planck's constant is too small? > > Evidence and and logic drive science. > > -Robert Molt > > On 06/01/2014 12:26 PM, V=C3=ADctor Lua=C3=B1a Cabal victor,fluor.quimica= .uniovi.es > wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal > > [victor-.-fluor.quimica.uniovi.es] > > On Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S h.rzepa: > imperial.ac.uk wrote: > >> Can I suggest that in future this poll be extended to indicate WHY an= y > person indicates they LIKE a functional? As we all know, the choice of > functional so often depends on what the property of interest is. > >> > >> I suggest initially a relatively short controlled list of properties, > >> which can then be extended by =E2=80=9Ccrowd sourcing=E2=80=9D. Prope= rties I have > >> in mind might be eg > >> > >> 1. Reaction barriers > >> 2. Normal mode analysis > >> 3. Chiroptical properties > >> 4. Hydrogen bonds > >> 5. Excitation energies > >> 6. Main group elements > >> 7. Transition metals > >> 8. Relativistic elements > >> 9. NMR shieldings, NMR couplings > >> 10. etc > >> > >> That way, we could find out eg the most liked functional for eg > >> looking at hydrogen bonds. That would be enormously helpful to > >> anyone looking to study eg hydrogen bonds. > > Dear Prof. Rzepa, > > > > I have a deep respect for your work, that I use to love, but in this > > case I dislike strongly the idea of deciding the use of a functional > > by popularity. There are plenty of examples in which the most popular > > route was not the best, just the easiest. It took decades, in many > > cases, to turn back wrong but popular decisions. Two candidates should > > be advised to create a safe road: the easiest AND the the best > > founded. Notice that the most popular is not in my list. Popularity > > can be obtained by well studied techniques that have nothing to do > > with any real measurement of quality. > > > > As for your list of properties it is very useful and I will keep it > > carefully. > > > > Best regards, > > Dr. V=C3=ADctor Lua=C3=B1a > > > > -- > > \|/ > > |^.^| > > +---!OO--\_/--OO!------------------------------+---------------------- > > +- > > ! Dr.V=C3=ADctor Lua=C3=B1a ! > > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > > ! e-mail: victor*fluor.quimica.uniovi.es ! > > ! phone: +34-985-103491 fax: +34-985-103125 ! > > +----------------------------------------------+ > > GroupPage : http://azufre.quimica.uniovi.es/ (being > > reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl > > .net/chemistry/sub_unsub.shtmlhttp:// > www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageht= tp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Steven Bachrach Semmes Distinguished Professor and Assistant VP for Special Projects Department of Chemistry Trinity University Phone: 210-999-7379 1 Trinity Place Fax: 210-999-7569 San Antonio, TX 78212 email: sbachrach]=[trinity.edu --047d7b6dc67aad7c3604fae0607d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I also think the poll has value in discerning trends,= especially new funtionals to appear on the list and ones that have fallen = down or off.

Steven

On Mon, Jun 2, 2014 at 9:17 AM, Abrash, Samuel s= abrash!^!richmond.edu <owner-che= mistry]=[ccl.net> wrote:

Sent to CCL by: "Abrash, Samuel" [sabrash..richmond.edu]
I think people are taking the words "popularity contest" too seri= ously. =C2=A0It's just a poll to find out what members of this listserv= e, who are mostly computational chemistry professionals, are using. =C2=A0I= agree that the absence of "why" makes this somewhat less useful.= =C2=A0However, I think it's useful because if I see a functional that = I don't know about used widely, I'm going to investigate it. =C2=A0= (Note not blindly use it, but investigate it.) =C2=A0Still the why is a use= ful bit of information. =C2=A0For =C2=A0example, I use M062X for many of my= calculations now, and if asked why, I'd say "because reviewers in= sisted that it's better for complexes than PBEPBE even though my result= s come out the same with either functional, and I wanted my paper published= ."

Best,
Sam

-----Original Message-----
> From: owner-chemistry+sabrash=3D=3Drichmond.edu . ccl.net [mailto:owner-= chemistry+sabrash=3D=3Drichmond.edu . ccl.net] On Behalf Of Laidig, Bill laidig.wd(_)pg.com
Sent: Sunday, June 01, 2014 8:45 PM
To: Abrash, Samuel
Subject: CCL: DFT14poll


Sent to CCL by: "Laidig, Bill" [laidig.wd=3Dpg.com] I strongly disagree with this position. = =C2=A0There are many scientifically valid reasons to know which functionals= are most popular among theoretical and computational chemists (who, I am a= ssuming, are the bulk of this mailing list). =C2=A0For example:

1. Even if a functional is clearly inferior to another, if it is used much = more in real calculations then there may be several reasons to use the infe= rior function:
=C2=A0 =C2=A0 =C2=A0a. It is likely more widely implemented meaning you hav= e a wider choice of programs
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0to use and ways to validate that the calc= ulations were =C2=A0performed correctly.
=C2=A0 =C2=A0 =C2=A0b. Wider use means that there is a larger statistical p= ool of data for assessing accuracy,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0etc. =C2=A0This is often much more import= ant than using a marginally better method. =C2=A0We
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0see this in the long-term popularity of m= ethods such as HF/3-21G, and B3LYP/6-31G*.
2. Highly accurate, but arcane theoretical methods make communication of re= sults difficult outside the expert community as the reader has little basis= for assessing the quality of results. =C2=A0I learned this the hard way in= my career in industry.

Most users of computational chemistry want to know what small handful of me= thods can be applied broadly to large classes of problems. =C2=A0As experts= , we are the group that is defining the next generation of standard methods= so I find it very useful to know in what directions we are heading. =C2=A0= Learning why we are using functionals can also let the developer of the &qu= ot;next big thing" know when their efforts to publicize and promote th= eir methodology has fallen short =C2=A0and inspire them to better efforts i= n the future.

Bill Laidig

-----Original Message-----
> From: owner-chemistry+laidig.wd=3D=3Dpg.com^ccl.net=
> [mailto:owner-chemistry= +laidig.wd=3D=3Dpg.com^= ccl.net] On Behalf Of Robe= rt
> Molt Jr r.molt.chemical.physics!=3D!gmail.com
Sent: Sunday, June 01, 2014 3:07 PM
To: Laidig, Bill
Subject: CCL: DFT14poll


Sent to CCL by: Robert Molt Jr [r.molt.chemica= l.physics]_[gmail.com] Sirs and Madames:

A "popularity contest" is anathema to science. =C2=A0The world sh= ould not weight the opinion of Rodney Bartlett and Robert Molt equally in c= oupled cluster theory.

Perhaps we should take a poll on what people think the first spherical harm= onic is? =C2=A0Or take a poll on whether Planck's constant is too small= ?

Evidence and and logic drive science.

-Robert Molt

On 06/01/2014 12:26 PM, V=C3=ADctor Lua=C3=B1a Cabal victor,fluor.quimica.uniovi.es w= rote:
> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal
> [victor-.-fluor.quimica.uniovi.es]
> On Sun, Jun 01, 2014 at 06:01:52AM +0000, Rzepa, Henry S h.rzepa:imperial.ac.uk wrote: >> Can =C2=A0I suggest that in future this poll be extended to indica= te WHY any person indicates they =C2=A0LIKE =C2=A0a functional? As we all k= now, the choice of functional so often depends on what the property of inte= rest is.
>>
>> I suggest initially a relatively short controlled list of properti= es,
>> which can then be extended by =C2=A0=E2=80=9Ccrowd sourcing=E2=80= =9D. Properties =C2=A0I have
>> in mind might be eg
>>
>> 1. Reaction barriers
>> 2. Normal mode analysis
>> 3. Chiroptical properties
>> 4. Hydrogen bonds
>> 5. Excitation energies
>> 6. Main group elements
>> 7. Transition metals
>> 8. Relativistic elements
>> 9. NMR shieldings, NMR couplings
>> 10. etc
>>
>> That way, we could find out eg the most liked functional for eg >> looking at hydrogen bonds. =C2=A0That would be enormously helpful = to
>> anyone looking to study eg hydrogen bonds.
> Dear Prof. Rzepa,
>
> I have a deep respect for your work, that I use to love, but in this > case I dislike strongly the idea of deciding the use of a functional > by popularity. There are plenty of examples in which the most popular<= br> > route was not the best, just the easiest. It took decades, in many
> cases, to turn back wrong but popular decisions. Two candidates should=
> be advised to create a safe road: the easiest AND the the best
> founded. Notice that the most popular is not in my list. Popularity > can be obtained by well studied techniques that have nothing to do
> with any real measurement of quality.
>
> As for your list of properties it is very useful and I will keep it > carefully.
>
> Best regards,
> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua= =C3=B1a
>
> --
> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 \|/
> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0|^.^|
> +---!OO--\_/--OO!------------------------------+----------------------=
> +-
> ! =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0Dr.V=C3=ADctor Lua=C3=B1a =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 !
> ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica =C2=A0 ! > ! Universidad de Oviedo, 33006-Oviedo, Spain =C2=A0 !
> ! e-mail: =C2=A0 victor*fluor.quimica.uniovi.es =C2=A0 =C2=A0 !
> ! phone: +34-9= 85-103491 =C2=A0fax: +34-985-103125 =C2=A0 !
> +----------------------------------------------+
> =C2=A0 GroupPage : http://azufre.quimica.uniovi.es/ =C2=A0(being
> reworked)http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= agehttp://www.ccl
> .net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_mess= agehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.= txt


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--
Steven Bachrach
Semmes Distingui= shed Professor and Assistant VP for Special Projects
Department of Chemistry
Trinity University =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Phone: 210-999-7379
1 Trinity Place =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Fax: 210-999-7569
San Antonio, TX 78212 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 email: sbach= rach]=[trinity.edu
--047d7b6dc67aad7c3604fae0607d--