From owner-chemistry@ccl.net Tue Oct 12 09:00:01 2010 From: "Wagener, M. \(Markus\) markus.wagener_-_spcorp.com" To: CCL Subject: CCL: Call for Papers: 9th International Conference on Chemical Structures (ICCS) Message-Id: <-42940-101012044242-18670-8sdgjAkOmJSYgSgCtUH87g++server.ccl.net> X-Original-From: "Wagener, M. \(Markus\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 12 Oct 2010 10:42:33 +0200 MIME-Version: 1.0 Sent to CCL by: "Wagener, M. \(Markus\)" [markus.wagener%x%spcorp.com] C A L L F O R P A P E R S 9th International Conference on Chemical Structures NH Leeuwenhorst Conference Hotel, Noordwijkerhout, The Netherlands 5-9 June 2011 Visit the conference website at www.int-conf-chem-structures.org for more information. The 9th International Conference on Chemical Structures (ICCS) is seeking presentations of novel research and emerging technologies for the following plenary sessions: o Cheminformatics > advances in structure representation > reaction handling and electronic lab notebooks (ELNs) > molecular similarity and diversity > chemical information visualization o Structure-Activity and Structure-Property Prediction > graphical methods for SAR analysis > industrialized and large-scale model building > multi-property prediction and multi-objective optimization o Structure-Based Drug Design and Virtual Screening > new docking and scoring approaches > improved understanding of protein-ligand interactions > pharmacophore definition and search > modeling of challenging targets o Analysis of Large Chemistry Spaces > mining of chemical literature and patents > design, profiling and comparison of compound collections and screening sets > machine learning and knowledge extraction from databases o Integrated Chemical Information > advances in chemogenomics > integration of medical and biological information > semantic technologies as a driver of integration > translational informatics o Dealing with Biological Complexity > analysis and prediction of poly-pharmacology > in-silico analysis of toxicology, drug safety, and adverse events > pathways and biological networks > druggability of targets Before and after the official conference program free workshops will be offered by several companies including BioSolveIT (www.biosolveit.de) and the Chemical Computing Group (www.chemcomp.com). Joint Organizers: o Division of Chemical Information of the American Chemical Society (CINF) o Chemical Structure Association Trust (CSA Trust) o Division of Chemical Information and Computer Science of the Chemical Society of Japan (CSJ) o Chemistry-Information-Computer Division of the Society of German Chemists (GDCh) o Royal Netherlands Chemical Society (KNCV) o Chemical Information Group of the Royal Society of Chemistry (RSC) o Swiss Chemical Society (SCS) We encourage the submission of papers on both applications and case studies as well as on method development and algorithmic work. The final program will be a balance of these two aspects. > From the submissions the program committee and the scientific advisory board will select about 30 papers for the plenary sessions. All submissions that cannot be included in the plenary sessions will automatically be considered for the poster session. Contributions can be submitted for any of the above and related areas, but we also welcome contributions in any aspect of the computer handling of chemical structure information, such as: o automatic structure elucidation o combinatorial chemistry, diversity analysis o web technology and its effect on chemical information o electronic publishing o MM or QM/MM simulations o practical free energy calculations o modeling of ADME properties o material sciences o analysis and prediction of crystal structures o grid and cloud computing in cheminformatics Visit the conference website at www.int-conf-chem-structures.org for more information, including details on procedures for online abstract submission and conference registration. The deadline for the submission of abstracts is 31 January 2011. We hope to see you in Noordwijkerhout. Keith T Taylor, ICCS Chair Markus Wagener, ICCS Co-Chair This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete. From owner-chemistry@ccl.net Tue Oct 12 09:35:00 2010 From: "Jason Rigby Jason.Rigby*monash.edu" To: CCL Subject: CCL:G: scalability of numerical frequency calculations in gaussian Message-Id: <-42941-101012092407-15354-fzYkB2w7oYhv4v55sza02A/./server.ccl.net> X-Original-From: Jason Rigby Content-Type: multipart/alternative; boundary=001485f6db2ccef6a304926b63f1 Date: Wed, 13 Oct 2010 00:23:40 +1100 MIME-Version: 1.0 Sent to CCL by: Jason Rigby [Jason.Rigby..monash.edu] --001485f6db2ccef6a304926b63f1 Content-Type: text/plain; charset=ISO-8859-1 Hello All, I'm just after some practical advice regarding the scalability and parallelisation of DFT (B3LYP) anharmonic frequency calculations in Gaussian. Does anyone have any idea at what point the performance vs number of processors relationship plateaus? In other words, what (generally speaking) is the highest number of processors one can use on a job like this before the performance gain (if indeed it isn't a loss due to network overhead etc.) is negligible? Cheers, Jason --001485f6db2ccef6a304926b63f1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello All,
I'm just after some practical advice regarding the scala= bility and=A0parallelisation=A0of DFT (B3LYP) anharmonic frequency calculat= ions in Gaussian. Does anyone have any idea at what point the performance v= s number of processors relationship plateaus? In other words, what (general= ly speaking) is the highest number of processors one can use on a job like = this before the performance gain (if indeed it isn't a loss due to netw= ork overhead etc.) is=A0negligible?

Cheers,
Jason
--001485f6db2ccef6a304926b63f1-- From owner-chemistry@ccl.net Tue Oct 12 10:09:00 2010 From: "Bjoern Baumeier baumeier+/-mpip-mainz.mpg.de" To: CCL Subject: CCL:G: Gaussian09 and external electric fields Message-Id: <-42942-101012092853-17751-nyLsWK86zf6yHin+yjOKHQ++server.ccl.net> X-Original-From: "Bjoern Baumeier" Date: Tue, 12 Oct 2010 09:28:45 -0400 Sent to CCL by: "Bjoern Baumeier" [baumeier-*-mpip-mainz.mpg.de] Hey all, I am trying to calculate some molecular properties under the influence of an external uniform electric field. In the Gaussian manual, I found that one should use the keyword field to do this but in its simplest version, i.e., field=x+1, it says that this is supposed to be a dipole field. I am a bit confused about the notation. Is this the right way to specify an external uniform field? Cheers, Bjoern From owner-chemistry@ccl.net Tue Oct 12 10:46:00 2010 From: "Avik Sanyal avik.sanyal#%#aci.uni-heidelberg.de" To: CCL Subject: CCL: accurate ionization energy & electron affinity Message-Id: <-42943-101012094343-439-wbIfHPeLgoddGzQlubMNvQ(-)server.ccl.net> X-Original-From: "Avik Sanyal" Date: Tue, 12 Oct 2010 09:43:42 -0400 Sent to CCL by: "Avik Sanyal" [avik.sanyal!A!aci.uni-heidelberg.de] Dear CCL-ers, I want ta calculate accurate ionization energies (IP) and electron affinities (EA) for atoms upto atomic number 30. Please suggest a good level of theory and a good basis set for doing such calculations. I know that energy level experimental data exist for a large number of atomic species, but I am interested in calculating such data that are not readily available (for eg., 4th electron affinity of Na etc). Any help would be appreciated. Regards Avik Sanyal From owner-chemistry@ccl.net Tue Oct 12 11:20:00 2010 From: "Yu Zhang spacyhunter#gmail.com" To: CCL Subject: CCL: Any program package can do non-integer no. of electrons calculation? Message-Id: <-42944-101012110153-27495-bTXbk1GmsQF8sskol5MgtA[#]server.ccl.net> X-Original-From: Yu Zhang Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Tue, 12 Oct 2010 11:01:34 -0400 Mime-Version: 1.0 Sent to CCL by: Yu Zhang [spacyhunter##gmail.com] hi, all, I was wondering if there is some public program package which can do calculations on systems with non-integer no. of electrons, e. g., a water molecule with 10.5 electrons. I used to use some in-house code to do such kind of calculations but now have no access to it. Could someone give me any suggestion? Thanks a lot! best regards Yu Zhang From owner-chemistry@ccl.net Tue Oct 12 11:55:00 2010 From: "Geoffrey Hutchison geoffh{:}pitt.edu" To: CCL Subject: CCL:G: Gaussian09 and external electric fields Message-Id: <-42945-101012114230-507-fHCrGHo0rsawQxH2erEMuQ[#]server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Tue, 12 Oct 2010 11:41:58 -0400 MIME-version: 1.0 (Apple Message framework v1081) Sent to CCL by: Geoffrey Hutchison [geoffh~!~pitt.edu] > In the Gaussian manual, I found that one should use the keyword field to do this but in its simplest version, i.e., field=x+1, it says that this is supposed to be a dipole field. I am a bit confused about the notation. Is this the right way to specify an external uniform field? This would be an external uniform field along the X axis, with strength of +1e-4 atomic units (e.g., 5.14e7 V/m). Gaussian allows more complicated fields, which is why the documentation might be confusing. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh() pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Tue Oct 12 13:39:00 2010 From: "Mikael Johansson mikael.johansson=-=helsinki.fi" To: CCL Subject: CCL: Any program package can do non-integer no. of electrons calculation? Message-Id: <-42946-101012133748-31419-2Eoq11JL2Tz8fvtKMoZ9kg(0)server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 12 Oct 2010 20:37:38 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson a helsinki.fi] Hello! On Tue, 12 Oct 2010, Yu Zhang spacyhunter#gmail.com wrote: > I was wondering if there is some public program package which can do > calculations on systems with non-integer no. of electrons, ADF can do it (but not with self-interaction correction, which at some point was why I checked it out), as well as Turbomole, and probably many other codes. Just use your favourite code and see what happens if you manually specify non-integer occupations or charge :-) In the case of ADF, it is even mentioned in the manual, so I guess it works "correctly". Haven't really checked the results from a Turbomole run, but at least it gives no error messages. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Tue Oct 12 14:27:00 2010 From: "Mikael Johansson mikael.johansson^-^iki.fi" To: CCL Subject: CCL: Any program package can do non-integer no. of electrons calculation? Message-Id: <-42947-101012132914-23019-2LeB1G4IdIaGmlh6ILO9IA_+_server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 12 Oct 2010 20:29:03 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson- -iki.fi] Hello! On Tue, 12 Oct 2010, Yu Zhang spacyhunter#gmail.com wrote: > I was wondering if there is some public program package which can do > calculations on systems with non-integer no. of electrons, ADF can do it (but not with self-interaction correction, which at some point was why I checked it out), as well as Turbomole, and probably many other codes. Just use your favourite code and see what happens if you manually specify non-integer occupations or charge :-) In the case of ADF, it is even mentioned in the manual, so I guess it works "correctly". Haven't really checked the results from a Turbomole run, but at least it gives no error messages. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/