From owner-chemistry@ccl.net Tue Feb 10 03:27:01 2009 From: "Marcel Swart marcel.swart||icrea.es" To: CCL Subject: CCL: ADF: excited-state optimization Message-Id: <-38587-090209184728-4727-tDtoY66VnUOFbklu+PJdng^server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 9 Feb 2009 22:42:13 +0100 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart\a/icrea.es] Using numerical gradients within the QUILD program. See: M. Swart and F.M. Bickelhaupt "QUILD: QUantum-regions Interconnected by Local Descriptions" J. Comput. Chem. 2008, 29, 724-734 Quoting "?? quarashino ~~ gmail.com" : > Dear All, > > How can one do excited-state geometry optimizations in ADF? > > Thanks in advance, > > Shino > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart%icrea.es marcel.swart%udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-chemistry@ccl.net Tue Feb 10 09:11:01 2009 From: "Jing Kong jkong],[q-chem.com" To: CCL Subject: CCL: Anouncing Q-Chem 3.2; Workshop reminder Message-Id: <-38588-090210083449-13528-DqdveY7D7AWtyZekbSnvtA]=[server.ccl.net> X-Original-From: "Jing Kong" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 10 Feb 2009 07:47:45 -0500 MIME-Version: 1.0 Sent to CCL by: "Jing Kong" [jkong*o*q-chem.com] Dear Colleague, We are happy to announce the release of Q-Chem 3.2, which adds quite a few latest developments in the field to our comprehensive and high-performance ab initio electronic structure program. Some of the new features in Q-Chem 3.2 are: 1. More accurate DFT calculations with long-range corrected functionals, especially for charge-transfer excitations, and with empirical van der Waals corrections; 2. DFT calculation with constrained charge distribution; 3. Minnesota's SM08 solvation model for energy and gradient; 4. Energy decomposition analysis based absolutely localized molecular orbitals; 5. New and improved post-HF methods including dual-basis MP2 and EOM-IP-CCSD; 6. Full QM/MM Hessian. For a complete list, please visit Q-Chem 3.2 page: http://www.q-chem.com/q-chem.htm. We encourage you to take advantage of the free evaluation offer on the website. We would also like to take the opportunity to remind you about our coming workshop on March 19th&20th at Pittsburgh Supercomputing Center. The workshop provides a great chance to meet with leading developers in the field and gain detailed knowledge about the latest methods and tools in computational quantum chemistry. Due to popular demand, we have extended our free offer for the workshop to February 19th. A detailed schedule has been added to the workshop webpage (http://www.q-chem.com/ws_hh.html). Please visit it for the details. I apologize if you receive multiple copies of this message. Happy Computing! Jing Kong **** Jing Kong, Ph.D., CEO&Chief Scientist, Q-Chem Inc. (http://www.q-chem.com) From owner-chemistry@ccl.net Tue Feb 10 13:09:01 2009 From: "Mikael Johansson mpjohans,,chem.au.dk" To: CCL Subject: CCL: virtual/versatile SMP (vSMP) for computational chemistry apps Message-Id: <-38589-090210123304-6118-ZVPwqScAmXlHoZYl9Mq1eg|-|server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 10 Feb 2009 17:57:45 +0100 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mpjohans_._chem.au.dk] Hello All! Does anyone have any experience with the virtual/versatile SMP (vSMP) technique in connection with real-world comp chem applications? With vSMP, you can apparently connect normal x86 boxes into seemingly one large, efficient SMP box: http://www.scalemp.com/prod/technology/ The company's web page (naturally) claims it works very well. I couldn't find any "real" benchmarks using this technology, however. Somehow it seems incredible that memory bandwidth wouldn't become a problem for a process/program that uses enough memory to span several individual PC boxes over just InfiniBand... If someone has any pointers or first-hand experience with real computations (even other than chemistry apps), I would be really glad to hear about it! Have a nice day, Mikael J. http://www.iki.fi/~mpjohans From owner-chemistry@ccl.net Tue Feb 10 14:32:01 2009 From: "Richard Tia richtiagh:+:gmail.com" To: CCL Subject: CCL: Problem with Spartan '06 Message-Id: <-38590-090210142913-793-XYVgB2RjeYZeuKEuwYdl4g++server.ccl.net> X-Original-From: "Richard Tia" Date: Tue, 10 Feb 2009 14:29:09 -0500 Sent to CCL by: "Richard Tia" [richtiagh%x%gmail.com] Hi all, I am running Spartan'06 for windows on a Dell Precision T3400 machine with the following specs: Intel Core 2 Quad CPU, 2.39GHz, 3.25 GB of RAM. Any attempt to generate an energy profile for an organometallic system I'm working on always generates an error which reads in part as: "RC = 111, internal error. SEGERR signal generated." Am I doing something wrong? Does anybody know a way out? Thanks in advance for any suggestions. Richard Tia Department of Chemistry KNUST, Kumasi Ghana From owner-chemistry@ccl.net Tue Feb 10 19:51:00 2009 From: "Lochana C Menikarachchi lochanac|a|yahoo.com" To: CCL Subject: CCL: Electron Transfer Rate Constant Message-Id: <-38591-090210194734-16282-kEKcGUzu402Gqrw1BGsY8A=-=server.ccl.net> X-Original-From: "Lochana C Menikarachchi" Date: Tue, 10 Feb 2009 19:47:31 -0500 Sent to CCL by: "Lochana C Menikarachchi" [lochanac.:.yahoo.com] Hi, I need to calculate electron transfer rate constant for a heme containing protein assembled in a self assembled monolayer. Is there any software package that can calculate various terms in the marcus equation for such a system. Any ideas on how to calculate heterogeneous electron transfer rate constants using existing software packages is appreciated. Thanks. best regards, Lochana From owner-chemistry@ccl.net Tue Feb 10 21:15:00 2009 From: "Antonio G. De Crisci antonio.decrisci+*+utoronto.ca" To: CCL Subject: CCL: using MacGAMESS on a cluster managed by 'Pooch' Message-Id: <-38592-090210211310-15573-vHw37uiVNlpHiuGnaViDIA_-_server.ccl.net> X-Original-From: "Antonio G. De Crisci" Date: Tue, 10 Feb 2009 21:13:07 -0500 Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci a utoronto.ca] Hello All, Im currently running a small computer 'cluster' using two 1.45 GHz Mac G4's Duals with OS X 10.3.9 linked directly to eachother via the ethernet jack (no ethernet switch needed in this case). Using the program called Pooch by Dauger Research, ( http://daugerresearch.com/pooch/whatis.shtml ) the parallel computing works great. Both computers see eachother and the two sample applications that comes with Pooch (Power Fractal and another program) runs much faster when launched in Pooch which use the two computer computer compared to just double clicking on it on one computer, as you would expect. However, when I try to run MacGAMESS, it only runs on one computer. When launching MacGAMESS via Pooch, the only thing that happens is that the "terminal" applications open on both computers but then of course when I type in the commands (i.e. ./gms input.inp) MacGAMESS only runs on one computer (CPU max on one computer while the other computer is at idle). The difference between luanching MacGAMESS and the other two sample applications that Pooch comes with, is that these two programs were executables and can be launched just by clicking on icon. My questions are: 1. Does anybody know if Pooch supports applications that are launched via the terminal? 2. Do I have make the gms file an executable file? 3. Also, do I have to put in some special parameters in the input file to let MacGAMESS know that its a parallel calculation? 4. Related to question #3 above, these computers have two processors (not two cores, I believe) do I have specify this in the GAMESS input file or do I specify it in Pooch for a total of 4 nodes? Thanks for you time, Antonio G. De Crisci University of Toronto From owner-chemistry@ccl.net Tue Feb 10 21:49:01 2009 From: "Mikael Johansson mpjohans{}chem.au.dk" To: CCL Subject: CCL: Electron Transfer Rate Constant Message-Id: <-38593-090210213641-24853-mK/JWMLXT3Xm0N2BMLug8Q[*]server.ccl.net> X-Original-From: Mikael Johansson Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Wed, 11 Feb 2009 03:36:24 +0100 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mpjohans##chem.au.dk] Hello Lochana! On Wed, 11 Feb 2009, "Lochana C Menikarachchi lochanac|a|yahoo.com" wrote: > I need to calculate electron transfer rate constant for a heme > containing protein assembled in a self > assembled monolayer. Is there any software package that can > calculate various terms in the marcus equation for such a system. If you want to do it (semi-)quantum mechanically, you have quite big a task ahead of you. For a good introduction to the parameters needed, see for example: Rosso and Dupuis, "Electron transfer in environmental systems: a frontier for theoretical chemistry", Theor. Chem. Acc. 116 (2006) 124-136. I think the most troublesome would be to get the electronic coupling done. At least NWChem has the capability of doing these sorts of calcs. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans