From owner-chemistry@ccl.net Sat Apr 25 02:52:01 2009 From: "Brian Salter-Duke brian.james.duke(~)gmail.com" To: CCL Subject: CCL: Computational Chemistry Wiki Message-Id: <-39160-090424200623-27868-8BGWz6bLCrYazSdRpU+21A##server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Sat, 25 Apr 2009 10:05:59 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke:+:gmail.com] Sabastian and others, I am not opposing the specific wiki. I support it. We have to get the difference between it and wikipedia right and I think you are mostly spot on. Where I think you are a little out is that you suggest you have to be an expert to contribute to wikipedia. Actually wikipedia does not much like experts or at least those who try to pull rank as experts. The best editors are those learning as post grad students. They know what is important and they know the sources and can use the sources appropriately referenced. Real experts tend to go off on their own hobby horses. If this is a repeat e-mail I apologize, but I got a message that it was not delivered. Brian. Sebastian Kozuch kozuchs^yahoo.com wrote: > The idea of a specific computational chemistry wiki is not to undermine > or compete with Wikipedia. The idea is to complement Wikipedia, blogs, > books and papers. Wikipedia is extremely helpful, and if I had the > knowledge I would have loved to contribute there. More than that, as far > as I’m concerned if you look for something basic like DFT in the new > wiki there should be only a reference to the entry in Wikipedia. > > But I cannot expect Wikipedia to have a specific entry on, let’s say, > BP86 or UFF. Neither I suppose we can add there a table with the mean > error of the different post-HF geometry bond lengths, or a list of the > programs that can run M06. But most of all, I’d like an up to date > encyclopedia where if I search for “MP4” it won’t appear with a > multimedia player. > > And, as Brian says, Wikipedia is not for self-publicity, and most of the > new methods that appear in computational chemistry cannot enter there > unless they are really fundamental methods. This takes years, and leave > most methods outside. > > Again, for those that are real specialists on traditional methods, I > encourage them to write in Wikipedia. But all the information that can > be useful only for computational chemists, I encourage to put it in this > specific wiki. > > Take into account that the same people of Wikipedia support the creation > of specific encyclopedias for specific communities. > > Again, if you like the idea and want to contribute, the page is > > > > http://computationalchemistry.wikia.com > > > > Maybe it will work, maybe not. But for sure it's worth to try it. > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > ..........Sebastian Kozuch........... > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > ...The Lise Meitner-Minerva Center... > .for Computational Quantum Chemistry. > ...Hebrew University of Jerusalem.... > .....kozuchs]*[yfaat.ch.huji.ac.il..... > http://yfaat.ch.huji.ac.il/kozuch.htm > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > > ------------------------------------------------------------------------ > *From:* Brian Salter-Duke brian.james.duke---gmail.com > > *To:* "Kozuch, Sebastian " > *Sent:* Friday, April 24, 2009 2:02:53 AM > *Subject:* CCL: Computational Chemistry Wiki > > > Sent to CCL by: Brian Salter-Duke [brian.james.duke:-:gmail.com > ] > Lukasz Cwiklik cwiklik]^[gmail.com wrote: > > Sent to CCL by: Lukasz Cwiklik [cwiklik..gmail.com] > > Dear Sebastian, > > I do not want to undermine your idea of a new wiki, however, this kind > > of wiki exist, it is simply in Wikipedia (see 'Computational > > Chemistry' article which covers a similar range of topics: > > http://en.wikipedia.org/wiki/Computational_chemistry). So maybe it > > would be better and easier to encourage CCL-ers to extend the existing > > Wikipedia articles in this topic. Also, the resulting information > > would be much more accessible for the general audience. > > Anyway, your idea to convince people to write something in the wiki > > system is very good. > > Best, > > Lukasz > > > > I word of caution about using wikipedia for the purposes proposed by the > original poster of this thread, from one of the people Henry referred to > who tries to upgrade, improve and protect the wikipedia articles on > computational chemistry. Wipedia has its own policies and guidelines. We > are writing an encyclopis based on what others have said. Everything > should be referenced. Original research is not allowed. So "new ones, > which implies that the authors of those methods are welcomed to make > self-publicity" is an absolute no-no. Anyone trying to do that, would > experience serious grief, with the material being promptly removed by > someone, possibly me. > > There is also the science wiki, which was the original a computational > chemistry wiki, as you can see from the URL it still has. Here is the > main QC entry point:- > > http://www.compchemwiki.org/index.php?title=Quantum_chemistry > > The original purpose was rather different from what is suggested here, > as it was to collect together QC results. It also not very active. > > I would encourage readers of CCL to help maintain and develop the > wikipedia pages, but I suggest you move in slowly and learn how the > place works. One problem with the CC and QC articles is that are often > dominated by physicists and become almost unintelligible to chemists. > They need to cover both physics and chemistry viewpoints. I sometimes > give up on these articles and edit something completely different as a > break from CC. I am happy to assist anyone. I am User:Bduke on wikipedia. > > Brian.> the strange characters on the top line to the ]*[ sign. You can also> > E-mail to subscribers: CHEMISTRY]*[ccl.net > or use: > > > E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net > or usehttp://www.ccl.net/chemistry/sub_unsub.shtml> > > From owner-chemistry@ccl.net Sat Apr 25 03:37:01 2009 From: "uzma mahmood mehmoodchemist[*]gmail.com" To: CCL Subject: CCL: GOLD_docking Message-Id: <-39161-090425033338-27150-Jj3cCTCu2GR0k5nchXhLog]*[server.ccl.net> X-Original-From: "uzma mahmood" Date: Sat, 25 Apr 2009 03:33:34 -0400 Sent to CCL by: "uzma mahmood" [mehmoodchemist##gmail.com] dear all subscriber any one can help me regarding docking on gold software by using covalent interaction all apply all the procedure as define in manual but i think i have some problem in input files so any one who has done this type of work so kindly help me resolve this problem thanks uzma From owner-chemistry@ccl.net Sat Apr 25 08:06:01 2009 From: "Rajagopalan S r.subramanian-,-ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: help needed Message-Id: <-39162-090425062601-23723-/U4zO9Z7t+sfBGToymCDgQ^^server.ccl.net> X-Original-From: "Rajagopalan S" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Sat, 25 Apr 2009 11:42:12 +0200 MIME-Version: 1.0 Sent to CCL by: "Rajagopalan S" [r.subramanian(~)ipc.uni-stuttgart.de] please copy and paste your % and # commands On Fri, 24 Apr 2009 10:32:57 -0400 "tamer sabry el-shazly t_sabry2005]^[hotmail.com" wrote: > > Sent to CCL by: "tamer sabry el-shazly" >[t_sabry2005|-|hotmail.com] > dear sir. > kindly to help me by answer the following; > 1- how can i overcome the abnormal termination of >gaussian calculation with G03W\11002exe and 15002exe > > 2- in spite of presence key word freq in my route input >the frequencies not calculated, only optimize the >structures without calculating the frequencies , how can >i overcome this problem > Thanks so much to help > recent computational chemist > tamer sabry > t_sabry2005=hotmail.com > > > > -= 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> > E-mail to administrators: CHEMISTRY-REQUEST . ccl.net or >use> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: >http://www.ccl.net/chemistry/searchccl/index.shtml> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > From owner-chemistry@ccl.net Sat Apr 25 14:44:01 2009 From: "David Eisenberg david.eisen]~[gmail.com" To: CCL Subject: CCL: Too many resonance structures in NRT Message-Id: <-39163-090425144304-10771-0liNHFWZWizZ2h0eC3Biwg(a)server.ccl.net> X-Original-From: "David Eisenberg" Date: Sat, 25 Apr 2009 14:43:00 -0400 Sent to CCL by: "David Eisenberg" [david.eisen%gmail.com] Dear CCL'ers, I'm trying to find the major resonance structures of a rather large polycyclic molecule, using the NRT (natural resonance theory) module in NBO 5.G (with PBE1PBE/6-31G*). The job fails because there are more resonance structures than what the computer memory can cope with. I've increased the alloted memory to the maximum, and it crashes still. But I don't need all these structures! I only want to look at the major ones. Is there a way of increasing the threshold, so the program ignores the structures that contribute less than so-and-so, and thus saves on memory? And if it's not possible, any suggestions on what I might try to find the major structures anyway? Thank you! David Eisenberg From owner-chemistry@ccl.net Sat Apr 25 16:50:01 2009 From: "Huo-Lei Peng horaldraman]_[gmail.com" To: CCL Subject: CCL:G: Questions about SAC-CI calculations. Message-Id: <-39164-090425025429-7423-oZK/3J9WR4n2ph98FALhQQ . server.ccl.net> X-Original-From: "Huo-Lei Peng" Date: Sat, 25 Apr 2009 02:54:25 -0400 Sent to CCL by: "Huo-Lei Peng" [horaldraman : gmail.com] Hi All: Recently, I'v been working on the calculations on a doublet radical, which has 11 carbon, nitrogen or oxygen atoms, using SAC-CI in Gaussian 03. It looks SAC-CI needs a lot of disk space and computer resource. In my case, the computation generated a huge rwf or scr file (up to several hundred GB) and failed finally. Could you give me any suggestion? Here is the input: %nprocshared=4 %mem=16GB %rwf=1.rwf,30gb,2.rwf,30gb,3.rwf,30gb,4.rwf,30gb,5.rwf,30gb,6.rwf,-1 # SAC-CI=(Full, MaxR2Op=1000000, AnionDoublet=(Nstate=3))/6-31G(d) ROH #P GFINPUT IOP(6/7=3) ---------------------------------------------------------------------- BTW, if I use CASSCF to calculate the doublet radical, how to select the active space? Initial open- shell calculation gave me alpha and beta orbitals. So how to select the orbitals in this case. Any suggestions will be highly appreciated Thanks. Huo-Lei Peng Department of Chemistry The Ohio State University 100 W. 18 Avenue Columbus, OH 43210 From owner-chemistry@ccl.net Sat Apr 25 20:07:00 2009 From: "Nuno A. G. Bandeira nuno.bandeira**ist.utl.pt" To: CCL Subject: CCL: Too many resonance structures in NRT Message-Id: <-39165-090425160419-11677-rJ6uWjhxiWd+5G17dcRIog%server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Type: multipart/mixed; boundary="=======AVGMAIL-49F363C50000=======" Date: Sat, 25 Apr 2009 20:25:56 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira,+,ist.utl.pt] --=======AVGMAIL-49F363C50000======= Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit David Eisenberg david.eisen]~[gmail.com wrote: > > The job fails because there are more resonance structures than what the > computer memory can cope with. I've increased the alloted memory to the > maximum, and it crashes still. But I don't need all these structures! I > only want to look at the major ones. Is there a way of increasing the > threshold, so the program ignores the structures that contribute less than > so-and-so, and thus saves on memory? And if it's not possible, any > suggestions on what I might try to find the major structures anyway? You must up the delocalisation threshold. Since the default is 1 kcal/mol you could try something like NRTTHR=10 or 20 and then go down as you please to get more resonance structures. Cheers, Nuno -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student % IST,Lisbon -- --=======AVGMAIL-49F363C50000======= Content-Type: multipart/alternative; boundary="=======AVGMAIL-49F363C50000=======" --=======AVGMAIL-49F363C50000======= Content-Type: text/plain; x-avg=cert; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Content-Description: "AVG certification" No virus found in this outgoing message. Checked by AVG - www.avg.com Version: 8.0.238 / Virus Database: 270.12.4/2080 - Release Date: 04/25/09 08= :29:00 --=======AVGMAIL-49F363C50000=======-- --=======AVGMAIL-49F363C50000=======--