From owner-chemistry@ccl.net Tue Mar 28 06:49:01 2006 From: "Eduardo Lemos de Sa edulsa/a\mkem.uu.se" To: CCL Subject: CCL: thermocromism Message-Id: <-31342-060328060456-22996-tO8kmUvP0ctaxS3yAabdFQ{=}server.ccl.net> X-Original-From: Eduardo Lemos de Sa Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 28 Mar 2006 12:13:29 +0200 MIME-Version: 1.0 Sent to CCL by: Eduardo Lemos de Sa [edulsa_+_mkem.uu.se] Sirs and Ladies I am starting a new research work where I am supposed to study thermocromic properties in organomethalic compounds. I will like hear your oppinions about what are the best approaches (methodology and softwares) in this isse. thank you very much in advance My best wishes Eduardo -- Eduardo Lemos de Sa Materials Chemistry Department - Uppsala University (Licensed by Departamento de Quimica - Universidade Federal do Parana) edulsa]*[mkem.uu.se or edulsa]*[quimica.ufpr.br phone: ++46 (18) 471 3747 From owner-chemistry@ccl.net Tue Mar 28 10:28:00 2006 From: "Roger Kevin Robinson r.robinson-#-imperial.ac.uk" To: CCL Subject: CCL: Free Conformational Analysis Software Message-Id: <-31343-060328085941-2880-VbpTwCKsLUDflnEjpc8CtA||server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 28 Mar 2006 14:56:22 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson()imperial.ac.uk] Hi, I was wondering if any one knew if there is any free conformation analysis software either for Linux or Windows. Ive been used to using Cerius2 (drieding) but this is no longer available to me. I tried Dynamol but it doesnt seem to be able to choose the lowest energy confermer. Although it can generate all confermers. Any advice would be appreciated. Roger From owner-chemistry@ccl.net Tue Mar 28 15:07:00 2006 From: "Mark Thompson mark::arguslab.com" To: CCL Subject: CCL: Comparison of Athelon and Pentium 4M ? Message-Id: <-31344-060328142108-7703-wXyCtGP3xji3lkSM5J/xXA%x%server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 28 Mar 2006 11:20:56 -0800 MIME-Version: 1.0 Sent to CCL by: Mark Thompson [mark,,arguslab.com] I have to compare some performance numbers between a couple of processors. Specifically, the Athelon MP 1800+ and a 2.4 GHz Pentium 4M laptop. I'm only interested in rough comparisons (e.g. "P4M is ~1.5x faster on the XXX benchmark than Athelon", etc.) I've poked around the web and have not found any good resources for these numbers. Any ideas or suggestions would be welcome. Thanks, Mark -- ------------------------ Mark Thompson mark]^[arguslab.com http://www.arguslab.com ------------------------ From owner-chemistry@ccl.net Tue Mar 28 15:47:00 2006 From: "Yu Adam Zhang yzhang[]chem.ubc.ca" To: CCL Subject: CCL:G: question about Gaussian03 PCM calculation Message-Id: <-31345-060328140927-6064-AnVNV+5trXLYwL7m4mI6kA-#-server.ccl.net> X-Original-From: "Yu Adam Zhang" Date: Tue, 28 Mar 2006 14:09:24 -0500 Sent to CCL by: "Yu Adam Zhang" [yzhang[-]chem.ubc.ca] hi, all I want to do some pcm calculations with Gaussian03. As many people complained on ccl, my opt calculation failed. Once I learned from one post on ccl that specifying the molecular cavity might help (using scrf=(read,...) and an additional input line). So I wrote my input file as following: %mem=500mb %nproc=2 b3lyp/6-31g** scrf=(pcm,solvent=h2o,read) opt title 0 1 C C 1 B1 .. ... D32 -1.25323616 D33 -121.20303534 end of molecular geometry specification RADII=UAKS (blank line) (end of input file) but this input file didn't work:(. It always gave a error message like: ...... Using the following non-standard input for PCM: 1 2 1.5 5 1.0 9 1.0 ------------------------------------------------------------------------------ The following wrong keyword(s) have been found: 1.0 ------------------------------------------------------------------------------ Error termination via Lnk1e in /usr/apps/g03_c02/g03/l301.exe at Mon Mar 27 17:26:26 2006. ...... What can I do to get out of mistake? Thank you very much if you can give me hand! Yu From owner-chemistry@ccl.net Tue Mar 28 16:53:01 2006 From: "Ross Walker ross%rosswalker.co.uk" To: CCL Subject: CCL:G: Comparison of Athelon and Pentium 4M ? Message-Id: <-31346-060328163314-5936-XWXgvD4UZrdoGA5ohIEz0g]_[server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Mar 2006 13:33:06 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross++rosswalker.co.uk] > I have to compare some performance numbers between a couple > of processors. > Specifically, the Athelon MP 1800+ and a 2.4 GHz Pentium 4M laptop. > > I'm only interested in rough comparisons (e.g. "P4M is ~1.5x > faster on > the XXX benchmark than Athelon", etc.) > > I've poked around the web and have not found any good resources for > these numbers. Adding the normal Caveat that performance is always a function of the type of job you want to run...: There are some Gaussian 98 numbers I ran a long time ago on various processors including an Athlon 1800XP which should be the same as an Athlon 1800MP (they only differ in the fact that one of the external bridges is lasered open on the XP version to stop it working parallel. If you close the bridge with some conductive paint it then reports itself as an 1800MP...) - see http://www.rosswalker.co.uk/benchmarks/gaussian_98_a7_proc_comparissons.html There aren't any 2.4GHz P4 M numbers on there unfortunately but the Gaussian input is there if you have access to such a machine running Gaussian you could get the numbers. > From just general experience I think you should be looking at a considerable speed difference for the P4M - of the order of 2x or more. The 2 MB cache of the P4M makes a big big difference. Plus the FSB speed is better. I hope this helps, All the best Ross /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross%a%rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. From owner-chemistry@ccl.net Tue Mar 28 17:27:03 2006 From: "Christian M Stegmann horizon:-:gwdg.de" To: CCL Subject: CCL: Announcement: 3rd International PhD Student Symposium - Horizons Message-Id: <-31347-060328155630-15712-Q0/ba8ktyANAsLcovOkC6g(!)server.ccl.net> X-Original-From: "Christian M Stegmann" Date: Tue, 28 Mar 2006 15:56:25 -0500 Sent to CCL by: "Christian M Stegmann" [horizon__gwdg.de] ======================================================================= Mark your calendar. You are invited to participate in the 3rd Horizons in Molecular Biology Symposium on September 14-16, 2006 at the Max Planck Institute for biophysical chemistry in Goettingen, Germany. http://www.horizons.uni-goettingen.de ======================================================================= Call for Abstracts: Horizons in Molecular Biology aims to provide deep insights into contemporary life science research and to encourage exchange among people from different biological science branches. We invite distinguished scientists from fields as diverse as structural biology, developmental biology, cell biology, neurobiology and stem cell research. By including such a diverse spectrum of topics we hope to broaden horizons and to inspire interdisciplinary discussions. Through the scientific and social events of the meeting we intend to improve the networking of Ph.D. students and young researchers from different parts of the world. The meeting will feature five sessions with invited lectures, two poster sessions, three sessions with student talks and includes an extensive social program. Confirmed invited speakers are: Structural Biology: Wolfgang Baumeister, Elena Conti, Louise Johnson, Nigel Unwin. Cell Biology: Philip Cohen, Ron Hay, Michael Rosenfeld, Joan Steitz. Neuroscience: Adriano Aguzzi, Barry Dickson, Oliver Hobert, Paul Sternberg. Developmental Biology: Philip Ingham, Ruth Lehmann, Alex Schier, Cliff Tabin. Stem Cell Research: Gerald Schatten, Hans Schoeler, Ian Wilmut. * Abstract submission opens on March 22, 2006. * Abstract submission deadline: August 1, 2006. For further details about registration, detailed program, abstract submission and contact information please visit our web page: http://www.horizons.uni-goettingen.de/ Please feel free to download the announcing poster from our website http://www.horizons.uni-goettingen.de/dl/horizons06.pdf Best regards, Christian Stegmann (On behalf of the the PhD Student Organizing Committee) --------------------------------------------------------- HORIZONS IN MOLECULAR BIOLOGY International PhD Student Symposium PhD Student Organizing Committee Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Gttingen Tel. +49 551 201 1585 Fax +49 551 201 1504 Email: horizon+/-gwdg.de www.horizons.uni-goettingen.de www.gpmolbio.uni-goettingen.de --------------------------------------------------------- From owner-chemistry@ccl.net Tue Mar 28 18:02:00 2006 From: "A ron Vandeputte Aaron.Vandeputte_+_Ugent.be" To: CCL Subject: CCL:G: Reaction path following with Gaussian Message-Id: <-31348-060328023538-14793-LNCNgr0bDlYURJXp41Dztw(_)server.ccl.net> X-Original-From: "A ron Vandeputte" Date: Tue, 28 Mar 2006 02:35:34 -0500 Sent to CCL by: "A ron Vandeputte" [Aaron.Vandeputte ~~ Ugent.be] In order to calculate tunneling corrections for H-abstractions, I'm trying to calculate the Hessian along the reaction path of the H-abstraction CH3 + CH4 -> CH4 + CH3 with g03 However, if I use as input line IRC(b3lyp/cbsb7,calcall,Cartesian,StepSize=1,MaxPoints=150,MaxCyc=50,verytight,forward) int=ultrafine nosymm calcultions fail to converge after 28 points. Gaussian iterates in cycles and the same sequence of energies is calculated till the maximum number of steps is exceeded. If I use calcfc in stead of calcall, g03 has no trouble to converge but then I don't get the wanted Hessian. I would be very grateful if someone could help me with my problem. Aron