From chemistry-request@server.ccl.net Wed Aug 14 05:26:31 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7E9QUl08894 for ; Wed, 14 Aug 2002 05:26:31 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 17euMC-0004ND-00 for chemistry@ccl.net; Wed, 14 Aug 2002 09:22:24 +0000 Date: Wed, 14 Aug 2002 09:22:24 +0000 (GMT) From: Szilveszter Juhos To: Computational Chemistry List Subject: Solaris cluster Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Members, Does anybody know a clustering method for Sparc Solaris 8 (SunOS tcf09 5.8 Generic sun4u sparc SUNW,Ultra-80) that can give ma a virtual single machine like Mosix? What I need is not a queueing system like GridEngine or Condor but something that can manage "gmake -j 16" on 4 machines with 4 cpus each. Thanks: Szilva From chemistry-request@server.ccl.net Wed Aug 14 07:35:49 2002 Received: from herodot ([217.116.225.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7EBZml11671 for ; Wed, 14 Aug 2002 07:35:49 -0400 Received: from douglas.i.netgroup.dk (dc0.fw.netgroup.dk [217.116.225.1]) by herodot (Postfix) with ESMTP id D93DD17A60 for ; Wed, 14 Aug 2002 13:35:47 +0200 (CEST) Date: Wed, 14 Aug 2002 13:36:02 +0200 (CEST) From: Kenneth Geisshirt Sender: kneth@douglas.i.netgroup.dk Reply-To: kenneth@geisshirt.dk To: Computational Chemistry List Subject: Re: CCL:Solaris cluster In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso-8859-1 Content-Transfer-Encoding: 8BIT On Wed, 14 Aug 2002, Szilveszter Juhos wrote: > What I need is not a queueing system like GridEngine > or Condor but something that can manage "gmake -j 16" on 4 machines with 4 > cpus each. You should take a look at ANTS: http://unthought.net/antsd Kneth -- Kenneth Geisshirt, M.Sc., Ph.D. http://kenneth.geisshirt.dk Grøndals Parkvej 2A, 3. sal kenneth@geisshirt.dk DK-2720 Vanløse +45 38 87 78 38 From chemistry-request@server.ccl.net Wed Aug 14 11:32:57 2002 Received: from mail1.rrz.Uni-Koeln.DE ([134.95.100.208]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7EFWvl18203 for ; Wed, 14 Aug 2002 11:32:57 -0400 Received: from campfire.rrz.Uni-Koeln.DE (IDENT:2897@campfire.rrz.Uni-Koeln.DE [134.95.19.27]) by mail1.rrz.Uni-Koeln.DE (8.12.3/8.12.2) with ESMTP id g7EFWrvN023324 for ; Wed, 14 Aug 2002 17:32:53 +0200 (MEST) Received: from localhost (acp64@localhost) by campfire.rrz.Uni-Koeln.DE (8.9.1a/8.9.1) with SMTP id RAA01468 for ; Wed, 14 Aug 2002 17:32:51 +0200 (MET DST) X-Authentication-Warning: campfire.rrz.Uni-Koeln.DE: acp64 owned process doing -bs Date: Wed, 14 Aug 2002 17:32:51 +0200 (MET DST) From: Johannes Weber To: CHEMISTRY@ccl.net Subject: g98: excited state densities via TDDFT ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Dear CCL members, I have a general question: Is it possible to calculate electron densities of excited states and/or excited state spin densities and/or transition densities with the TDDFT method ? With respect to the TDDFT implementation in g98 this general question splits up into several concrete questions: Which density (ground state or excited state) will be written to the checkpoint file if I specify the DENSITY keyword in the route section together with TD(Root=1) ? -- The g98 manual is not very explicit about this point. If I look at the formatted checkpoint file I find two densities, named the "Total SCF Density" and "Total CI Rho(1) Density". What densities are given here? I was not able to extract the Total CI Rho(1) Density with the cubegen utility. Is this possible? Thanks in advance for all answers. If there is interest I will summarize them, of course. With kind regards, :-)ohannes --------------------------------------------------------------------- | Johannes Weber | Email: | | Universitaet zu Koeln | Johannes.Weber@uni-koeln.de | | Institut fuer Theoretische Chemie | tel: 0049-(0)221-470-4812 | | Luxemburger Str. 116 | fax: 0049-(0)221-470-5144 | | 50939 Koeln | | --------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Aug 14 14:15:14 2002 Received: from concord.org (IDENT:root@[4.19.234.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7EIFEl23131 for ; Wed, 14 Aug 2002 14:15:14 -0400 Received: from notes.concord.org (notes.concord.org [4.19.234.34]) by concord.org (8.11.6/8.11.6) with SMTP id g7EIFEx02363 for ; Wed, 14 Aug 2002 14:15:14 -0400 Received: by notes.concord.org(Lotus SMTP MTA v4.6.7 (934.1 12-30-1999)) id 85256C15.00638F55 ; Wed, 14 Aug 2002 14:07:27 -0400 X-Lotus-FromDomain: CONCORD CONSORTIUM From: qxie@notes.concord.org To: chemistry@ccl.net Message-ID: <85256C15.00638E14.00@notes.concord.org> Date: Wed, 14 Aug 2002 14:07:23 -0400 Subject: Annoucement: Concord Modeler v1.0 - Molecular simulation software for education Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear CCLers, Molecular simulation methods are useful in solving R&D problems in chemical and pharmaceutical industries. Techniques like molecular graphics, energy minimization, Monte Carlo and molecular dynamics have become valuable tools for materials and drug design. Surprisingly, these techniques have been found particularly useful in K-12 education in the US. Being a company pioneering on innovative educational technology, we have been developing molecular simulation tools specialized for education, and have done extensive field tests in schools. Our research results show that kids have significantly more cognitive gains by learning with interactive molecular models put in an appropriate pedagogical context, than learning in a more traditional way involving use of non-modeling multimedia such as Flash animations. There is constantly a gap between research and education in the history of science. This problem might be much less severe in Aristotle's time than in today, when the gap is unprecedentedly enlarging. Molecular simulation turns out to be one of the few fields that demonstrate an excellent opportunity to bridge the gap. This will be a very attractive research direction, considering the strategic importance of molecular-level science to the competitiveness of our future labor forces. Many of the CCLers will ask the following question: What makes an educational application different from a research one? First of all, educational applications require high-level interactivities, which in the case of molecular dynamics simulation are based on real-time computation, real-time user manipulation and dynamical visualization. In academic research, this type of computing is called interactive molecular simulation by, for example, Prof. Klaus Schulten's group. The difference here is that in an educaitonal setting, everything has to be done on a single microcomputer, and a user's action on a molecular system must be responded as promptly as possible. This requirement typically limits the number of atoms in a model to be in the hundreds in a classical molecular dynamics simulation. Second, educators always complain that monolithic applications such as the ones molecular simulation experts are using ( e.g. Cerius 2 or the lightweight WebLab Viewer, etc.) are too complicated to use, and lack the flexibility needed to organize models in an educational context (usually a sequence of guided activities with simplified user interfaces) and present them in an easy-to-understand form on various platforms. Funded by the National Science Foundation, we have developed a tool called Concord Modeler that we are pleased to share here. The Concord Modeler v1.0 can be downloaded at the following URL: http://workbench.concord.org/modeler/index.html The features of the Concord Modeler v1.0 are: 1) It is written in 100% Java, hence it runs on different platforms (currently Red Hat Linux and Windows OS). 2) It is, and will be, free and open-source, hence you can use the nuts and bolts in our API. 3) It is a Web browser which delivers models in XML format, hence it is content-rich and virus-proof. Because it is Web-based, your model will be seen and commented by visitors. Thus you can collaborate with other people on a simulation project. 4) It is an authoring tool which you can use to write your own curricula with models embedded in the context and publish on the Web. 5) You can do atomistic modeling using AMBER/CHARMm-like force fields, and non-atomistic modeling using generalized Gay-Berne force fields. You can easily create and manipulate objects. For example, a triatomic molecule can be constructed by assigning bond-stretching and angle-bending potentials to the three atoms. The model builder allows you to construct systems ranging from Lennard-Jones solids to liquid crystals and to polymers. 6) You can do NVE, NVT and NPT, and switch between these protocols. 7) Bond-crossing periodic boundary conditions in one or both directions are supported. 8) You can exert electromagnetic and gravitational fields. You can use external fields to study, for example, electrolysis or ion transport in an electric field. 9) You can create a time series for any property of the model and plot them instantly using a graph tool integrated in the Concord Modeler. 10) You can record a simulation and save it as a movie. The movie is a collection of coordinate, velocity, and higher order time series, a mechanism that allows you to track a single object or property when playing back a recorded simulation. 11) You can save the whole simulation and preserve almost all settings, and restore them later. This feature is particularly useful when you embed a simulation in a curriculum. 12) The molecular dynamics simulation engine is controlled by a task manager. You can add a job to or remove a job from the task pool. This mechanism allows you to create customized jobs. ...and much more. Limitations: 1) It is 2D. ---- We have built our own molecular graphics engine using Java3D and will incorporate it into the Concord Modeler. In education, 2D models have been proven very helpful because it shields students from the complexity of stereo reasoning. What is more, many physical mechanisms can be simulated using a cartoonized 2D model. 2) It is slow. ---- Yes, when you have a lot of particles. We focus on low-end uses. 3) It does not do quantum mechanics. ---- Yes. Perhaps the tight-binding approximation (TBMD) would be a good solution. In closing, students of today are scientists of tomorrow. The molecular simulation and modeling community will benefit if more of the beauty and power grown in the field of computational chemistry can be delivered to kids and deeply appreciated by them. As the developer, we would greatly appreciate your support and help. Your comments and opinions are extremely important to helping us improve this product and carry out research in this directioin. Q. Xie, PhD The Concord Consortium Inc. 10 Concord Crossing, Suite 300 Concord, MA 01742 From chemistry-request@server.ccl.net Wed Aug 14 12:19:27 2002 Received: from web12303.mail.yahoo.com ([216.136.173.101]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7EGJQl19610 for ; Wed, 14 Aug 2002 12:19:27 -0400 Message-ID: <20020814161926.65821.qmail@web12303.mail.yahoo.com> Received: from [212.25.107.106] by web12303.mail.yahoo.com via HTTP; Wed, 14 Aug 2002 09:19:26 PDT Date: Wed, 14 Aug 2002 09:19:26 -0700 (PDT) From: omar Deeb Subject: contributions of atomic orbitals To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-433807189-1029341966=:65572" --0-433807189-1029341966=:65572 Content-Type: text/plain; charset=us-ascii Hi ccl users, I have a new graduate student in computational chemistry and he wants to calculate the different contributions of atomic orbitals of the different atoms in the tested molecule to the molecular orbitals. He is using Hyperchem software, so please if any one can help him in this type of calculation using hyperchem or any other free software. Thanks a lot Omar --------------------------------- Do You Yahoo!? HotJobs, a Yahoo! service - Search Thousands of New Jobs --0-433807189-1029341966=:65572 Content-Type: text/html; charset=us-ascii

Hi ccl users,

I have a new graduate student in computational chemistry and he wants to

calculate the different contributions of atomic orbitals of the different atoms in the tested molecule to the molecular orbitals.

He is using Hyperchem software, so please if any one can help him in this

type of calculation using hyperchem or any other free software.

Thanks a lot

Omar


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