From owner-chemistry@ccl.net Wed Sep 7 08:57:00 2011 From: "Francisco Nu ez fnunez]=[klingon.uab.es" To: CCL Subject: CCL:G: DoVacuum option in G09 Message-Id: <-45407-110907062425-14885-DbKde6W2pgQZ0RioDgrlQQ#,#server.ccl.net> X-Original-From: "Francisco Nu ez" Date: Wed, 7 Sep 2011 06:24:22 -0400 Sent to CCL by: "Francisco Nu ez" [fnunez!=!klingon.uab.es] Dear CCL members. I'm trying to do a solvent calculation in Gaussian09 with the "DoVacumm" option to the SCRF method in order to calculate DeltaG solvation values, according to the G09 manual (http://gaussian.com/g_tech/g_ur/k_scrf.htm). I think this "DoVacumm" option replaces the old "SCFVAC" in G03, but the output file does not show any line with other values than the total energy in solution, that is, the SCF energy in solution with all corrections: Error on total polarization charges = 0.01687 SCF Done: E(RM06L) = -117.920383609 A.U. after 11 cycles Convg = 0.8498D-08 -V/T = 2.0052 KE= 1.173140244871D+02 PE=-4.142721974027D+02 EE= 1.082786096641D+02 This is a part of the input line: %mem=XXmw %nproc=XX #p m06l/6-311++g** 5d scrf=(cpcm,solvent=dichloromethane,read,DoVacuum) Can anyone say me why the dovacuum option does not work or is there any error with my input file ?? Thanks in advance !!! Francisco Nuez Zarur Autonomous University of Barcelona Spain From owner-chemistry@ccl.net Wed Sep 7 09:32:00 2011 From: "Andras Borosy andras.borosy---givaudan.com" To: CCL Subject: CCL: comparison of ab initio packages? Message-Id: <-45408-110907042034-22765-ndbYucavkZiIEopqY6LTlw:_:server.ccl.net> X-Original-From: Andras Borosy Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Date: Wed, 7 Sep 2011 10:20:15 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy|a|givaudan.com] Dear Colleagues, Might you suggest me publications about performance comparisons of ab initio packages in optimum geometry and TS computations of small organic and/or organometallic molecules? Many thanks, Dr. András Péter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf - Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com From owner-chemistry@ccl.net Wed Sep 7 11:33:00 2011 From: "Herbert Fruchtl herbert.fruchtl]|[st-andrews.ac.uk" To: CCL Subject: CCL: comparison of ab initio packages? Message-Id: <-45409-110907104900-11159-T6LRId/j8ATa682wA+PshA-*-server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 07 Sep 2011 15:44:44 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl]-[st-andrews.ac.uk] The licence for most of the commercial and even some of the free packages explicitly forbids publishing this sort of information. You can try to start a discussion on this list, but that will immediately be drowned out by shouts of "you should of course have used this or that obscure input flag in this case". Having created several of these comparisons in internal reports when working at a computer vendor, I can also attest that it's not straight-forward. Default accuracy settings (integral cutoffs, convergence thresholds, DFT grids) can make a program look fast when it is indeed just sloppy. You can usually set this in the input to some extent, but not exactly, and it's difficult to agree on a "reasonable" level of accuracy. Good luck, Herbert On 07/09/11 09:20, Andras Borosy andras.borosy---givaudan.com wrote: > > Sent to CCL by: Andras Borosy [andras.borosy|a|givaudan.com] > > Dear Colleagues, > > Might you suggest me publications about performance comparisons of ab > initio packages in optimum geometry and TS computations of small organic > and/or organometallic molecules? > > Many thanks, > > Dr. András Péter Borosy > Scientific Modelling Expert > > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf - > Switzerland > T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Wed Sep 7 12:49:00 2011 From: "Gerard Pujadas gerard.pujadas() gmail.com" To: CCL Subject: CCL: Suggestions for running virtual screening and cheminformatics programs on the cloud Message-Id: <-45410-110907124212-15478-UZ1TQc86t5Y7AiMc9n8K8w*server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=001517478cbe46986a04ac5c8fae Date: Wed, 7 Sep 2011 18:37:27 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas()gmail.com] --001517478cbe46986a04ac5c8fae Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL subscribers, we are thinking in performing virtual screening searches (*e.g.*protein-ligand docking and pharmacophore-based searches) on a cloud computing service in order to speed up the calculations. Basically the software programs we use belong to the Schr=F6dinger suite (*i.e.* Glide an= d Phase). Then, we would appreciate very much if, according to your experience, you could suggest us some cloud computing services. Any comment on this subject will be highly appreciated With many thanks in advances Yours sincerely Gerard --=20 Gerard Pujadas http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22 Nutrigenomics Research Group (now on sabatic leave at http://www.ctns.cat) phone +34 977 55 (9565) Biochemistry and Biotechnology Department Office 106, Building N4, Campus Sescelades Universitat Rovira i Virgili Tarragona, Catalonia --001517478cbe46986a04ac5c8fae Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL subscribers,

we are thinking in performing virtual screenin= g searches (e.g. protein-ligand docking and pharmacophore-based sear= ches) on a cloud computing service in order to speed up the calculations. B= asically the software programs we use belong to the Schr=F6dinger suite (i.e. Glide and Phase).

Then, we would appreciate very much if, according to your experience, y= ou could suggest us some cloud computing services.

Any comment on th= is subject will be highly appreciated

With many thanks in advances
Yours sincerely

Gerard
--
Gerard Pujadas
http://bio= quimica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomics Research Group (= now on sabatic leave at h= ttp://www.ctns.cat)
phone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Off= ice 106, Building N4, Campus Sescelades
Universitat Rovira i Virgili
= Tarragona, Catalonia
--001517478cbe46986a04ac5c8fae-- From owner-chemistry@ccl.net Wed Sep 7 15:26:00 2011 From: "Close, David M. CLOSED**mail.etsu.edu" To: CCL Subject: CCL: comparison of ab initio packages? Message-Id: <-45411-110907141159-26306-oeEqXTleQjruy5Zunf97dA!=!server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 7 Sep 2011 18:11:40 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED:mail.etsu.edu] Andras: This is an interesting question, but it is not clear that this group can provided a satisfactory answer. Some vendors license software with the caveat that one is not to compare their results with the results of others. So there are basic legal issues here. Beyond this one could run the same input parameters on two different platforms and compare the answers. But here there is another problem. It is not trivial to know what exactly two different programs are actually doing. One would need to know the convergence criteria used on each platform. So simple things like "faster" may just mean less accuracy. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu!=!ccl.net [mailto:owner-chemistry+closed==etsu.edu!=!ccl.net] On Behalf Of Andras Borosy andras.borosy---givaudan.com Sent: Wednesday, September 07, 2011 4:20 AM To: Close, David M. Subject: CCL: comparison of ab initio packages? Sent to CCL by: Andras Borosy [andras.borosy|a|givaudan.com] Dear Colleagues, Might you suggest me publications about performance comparisons of ab initio packages in optimum geometry and TS computations of small organic and/or organometallic molecules? Many thanks, Dr. András Péter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf - Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.comhttp://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 Wed Sep 7 21:51:00 2011 From: "Horkel, Ernst ehorkel__ioc.tuwien.ac.at" To: CCL Subject: CCL:G: AW: G: Gaussian09 frequency job failed Message-Id: <-45412-110907170211-9639-3rhFGM9xtKC7TtLdP1a14A(a)server.ccl.net> X-Original-From: "Horkel, Ernst" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 7 Sep 2011 23:02:04 +0200 MIME-Version: 1.0 Sent to CCL by: "Horkel, Ernst" [ehorkel*ioc.tuwien.ac.at] Hello, I do not know if you already have a solution to your problem. If yes, please post it at CCL, if not, try to add: SCF=noincfock to your input line. It seems to be an oszillating problem, maybe this helps. If it helps, please post it to CCl, if not, post it too :-) Good luck, Ernst _______________________________________________ Univ.Ass. Dipl.-Ing. Dr.techn. Ernst Horkel Institute of Applied Synthetic Chemistry, Vienna University of Technology          Tel.: +43-1-58801-163609 Getreidemarkt 9/163OC,                         +43-664-60588-7122 A-1060 Vienna, Austria                   Fax:  +43-1-58801-15499 email: ehorkel*ioc.tuwien.ac.at -----Ursprüngliche Nachricht----- Von: owner-chemistry+ehorkel==ioc.tuwien.ac.at*ccl.net [mailto:owner-chemistry+ehorkel==ioc.tuwien.ac.at*ccl.net] Im Auftrag von Francisco Nu ez fnunez%a%klingon.uab.es Gesendet: Mittwoch, 24. August 2011 13:54 An: Horkel, Ernst Betreff: CCL:G: Gaussian09 frequency job failed Sent to CCL by: "Francisco Nu ez" [fnunez . klingon.uab.es] Hi all, I have a problem with a frequency calculations in Gaussian09. I am doing a freq calculations on a large systems (1247 basis functions, basis set 6-311+G(d,p)) and the calculations start apparently well, but suddenly the job dies without any error warning. This is a the final part of the .out file: 15 vectors produced by pass 48 Test12= 1.81D-13 1.00D-09 XBig12= 3.97D-15 1.57D-09. 14 vectors produced by pass 49 Test12= 1.81D-13 1.00D-09 XBig12= 4.15D-15 1.43D-09. 14 vectors produced by pass 50 Test12= 1.81D-13 1.00D-09 XBig12= 8.50D-15 2.22D-09. 14 vectors produced by pass 51 Test12= 1.81D-13 1.00D-09 XBig12= 7.86D-15 1.91D-09. 14 vectors produced by pass 52 Test12= 1.81D-13 1.00D-09 XBig12= 5.79D-15 1.61D-09. 14 vectors produced by pass 53 Test12= 1.81D-13 1.00D-09 XBig12= 8.42D-15 1.91D-09. 14 vectors produced by pass 54 Test12= 1.81D-13 1.00D-09 XBig12= 7.61D-15 2.17D-09. 14 vectors produced by pass 55 Test12= 1.81D-13 1.00D-09 XBig12= 1.46D-14 2.64D-09. 14 vectors produced by pass 56 Test12= 1.81D-13 1.00D-09 XBig12= 7.57D-15 1.98D-09. 14 vectors produced by pass 57 Test12= 1.81D-13 1.00D-09 XBig12= 1.06D-14 2.29D-09. 14 vectors produced by pass 58 Test12= 1.81D-13 1.00D-09 XBig12= 9.83D-15 2.45D-09. 14 vectors produced by pass 59 Test12= 1.81D-13 1.00D-09 XBig12= 9.99D-15 2.14D-09. 14 vectors produced by pass 60 Test12= 1.81D-13 1.00D-09 XBig12= 5.35D-15 1.63D-09. 6 vectors produced by pass 61 Test12= 1.81D-13 1.00D-09 XBig12= 2.63D-15 1.41D-09. Applied DIIS recursively to reduced A of dimension 8080. Mon Aug 22 04:25:03 CEST 2011 I have tried to run the calculations by splitting the RWF scrath file but all attempts were unsuccessful. I appreciate any help Francisco Nuez Zarur Autonomous University of Barcelona Spainhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt