From chemistry-request@ccl.net Fri Jun 3 03:15:15 2005 Received: from mailgateway1.uni-freiburg.de (mailgateway1.uni-freiburg.de [132.230.2.211]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j537F9Qh025034 for >ccl.net>; Fri, 3 Jun 2005 03:15:10 -0400 Delivery-date: Fri, 03 Jun 2005 09:15:09 +0200 Received: from waugh.imtek.uni-freiburg.de ([132.230.168.49]) port 58254 by mailgateway1.uni-freiburg.de with esmtp (Exim 4.50 #1 built 18-Feb-2005 14:34:25 running on Gentoo) id 1De6Oa-0004qa-6F for chemistry<>ccl.net; Fri, 03 Jun 2005 09:15:08 +0200 Mime-Version: 1.0 (Apple Message framework v622) Content-Transfer-Encoding: 7bit Message-Id: <8049e35ece47ba1f41dfae0fc4e862b6<>imtek.uni-freiburg.de> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed To: chemistry<>ccl.net From: Evgenii Rudnyi >imtek.uni-freiburg.de> Subject: CCL:Linear ODEs in Molecular Simulation Date: Fri, 3 Jun 2005 09:13:38 +0200 X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello, At present, I am working in the area of model reduction http://www.imtek.uni-freiburg.de/simulation/mor4ansys/ ModelOrderReduction.html It allows us to find a low-dimensional approximation to a large-scale system of ordinary differential equations. My current applications are finite element models. I am wondering if there are interesting applications in molecular simulation with a high-dimensional system of linear ODEs. Well, the trick is that the system should be linear. Unfortunately, an application of model reduction to classical molecular dynamics happens not to be straightforward. Best wishes, Evgenii Rudnyi -- IMTEK: Institute of Microsystem Technology Simulation of Microsystems Freiburg University Georges-Koehler-Allee 103 D-79110 Freiburg i. Br. Germany Tel. (+49 761) 203 7383 Fax (+49 761) 203 7437 http://www.imtek.uni-freiburg.de/simulation/ http://Evgenii.Rudnyi.Ru/ From chemistry-request@ccl.net Fri Jun 3 01:11:10 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j535BAiA021247 for ; Fri, 3 Jun 2005 01:11:10 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j535B9ba021246 for chemistry #%# ccl.net; Fri, 3 Jun 2005 01:11:09 -0400 Date: Fri, 3 Jun 2005 01:11:09 -0400 Message-Id: <200506030511.j535B9ba021246 #%# server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request #%# ccl.net using -f From: "Gustavo, , Mercier" To: chemistry #%# ccl.net X-Web-Message-Number: 050603010905-21169 Subject: W:gOpenMol and Gamess MO plotting X-Spam-Status: No, score=-0.6 required=5.0 tests=ALL_TRUSTED, FORGED_YAHOO_RCVD autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi! I am interested in plotting MO's computed using GAMESS-US. I've tried several programs with limited succes (molden, molekel, orbdraw) and now I am trying gOpenMol. Looking at the manual etc I need to generate a cube file that will be converted to the plt format read by gOpenMol using a plugin. However, it is not clear to me how to generate the cube file using GAMESS-US. GAMESS-US can compute a variety of properties, ie. electron density, electrostatic potential, etc. but I don't see an option for MO's. Moreover, these are computed either a set of user defined points (option POINTS), in a plane (option GRID), and as multiples of the van der wall surface (option PDC). There is no option for a 3D cube like gaussian's cube. Obviously, you can take the GRID or POINTS options and generate a cube from these, but then you have to find out the format expected by the plugin, i.e. what axis run fastest, etc. Any one willing to shed some light on how to proceed before I engage in writing code to do some of this stuff? 1) How do you generate the 3D cube using GAMESS-US? 2) Is it possible to plot GAMESS-US MO's using gOpenMoL? I do have the MO's from running a SCF run, but I would like to know if it is possible to "coax" GAMESS-US into computing the cube data needed by gOpenMol. Thanks! G. Mercier gamercier #%# yahoo.com gustavom #%# baylorhealth.edu