From chemistry-request@server.ccl.net Sat Jul 28 04:11:30 2001 Received: from mailgate3.cinetic.de ([212.227.116.80]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6S8BT526502 for ; Sat, 28 Jul 2001 04:11:29 -0400 Received: from web.de (fmomail02.dlan.cinetic.de [172.20.1.46]) by mailgate3.cinetic.de (8.11.2/8.11.2/SuSE Linux 8.11.0-0.4) with SMTP id f6S8BO618321 for chemistry@ccl.net; Sat, 28 Jul 2001 10:11:28 +0200 Date: Sat, 28 Jul 2001 10:11:28 +0200 Message-Id: <200107280811.f6S8BO618321@mailgate3.cinetic.de> MIME-Version: 1.0 Organization: http://freemail.web.de/ From: "Joerg Muehlbacher" To: chemistry@ccl.net Subject: CCL: Molecular dynamics at different temperatures Precedence: fm-user Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f6S8BU526528 Dear CCL'ers, I am performing MD simulations of small organic molecules (ca. C25H25NO3) with the MM3 and the Tripos force field both implemented in SYBYL (for parameters see below) in order to investigate barriers which should be overcome at room temperature. (We know this because of NMR experience, 'chemical intuition' and ab-initio calculations of these barriers). The simulations are carried out at the following temperatures: 300K, 400K, 500K, 600K, 700K, 800K, 900K, 1000K. I have observed that several of the namely barriers are surmounted for the first time in a simulation at high temeratures (eg. 800K, 900K)! Now i'm interested in how to correlate real and virtual temperature. I would be deeply grateful for all hints, literature, explanations etc. on this topic. Thanks for all help, Jörg ps here are my parameters: MM3: simulation length: 500 ps; timestep: 2 fs; bath coupling: 0.1; SHAKE: 0.01; dielectric constant: 1; recording geometry every 0.5ps -> 1000 geometries Tripos: simulation length: 500 ps; timestep: 0.5 fs; bath coupling: 0.1; no shake; dielectric constant: 13; recording geometry every 0.5ps -> 1000 geometries ______________________________________________________________________________ Jetzt und nur hier Ihr original PREMIERE WORLD SportPaket plus 100 Euro ExtraPrämie: http://premiere.web.de From chemistry-request@server.ccl.net Fri Jul 27 18:53:47 2001 Received: from lozen.uit.no ([129.242.5.254]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6RMrk503171 for ; Fri, 27 Jul 2001 18:53:46 -0400 Received: from james.chem.uit.no (james.Chem.Uit.No [129.242.24.111]) by lozen.uit.no (8.11.2/8.11.2) with ESMTP id f6RMriM18533 for ; Sat, 28 Jul 2001 00:53:45 +0200 (METDST) Received: from chem.uit.no (uran.Chem.Uit.No [129.242.24.167]) by james.chem.uit.no (8.9.3/8.9.3) with ESMTP id AAA764604 for ; Sat, 28 Jul 2001 00:52:06 +0200 (CEST) Sender: tsaue@chem.uit.no Message-ID: <3B61F0F7.9E01248B@chem.uit.no> Date: Sat, 28 Jul 2001 00:53:43 +0200 From: Trond Saue X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.3-20mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: Orbital interactions in 2001 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I checked out Amazon books website discussing the classic "Orbital Interactions in Chemistry" by Thomas A. Albright, Jeremy K. Burdett, and Myung-Hwan Whangbo. I found the following customer review: "Yes, this book is out-of-date, if you say. But the whole diagrams and symbols are already placed itself as the canon of this field. If you are an undergraduate chemistry major, you can see much ados about MO in recent texts are truly indebted to this book. You can also feel Hoffmann's friendly approaches. Hwangbo, et al are direct succesor of the spirit of Hoffmann school!" It would be interesting to hear CCLers viewpoint of what books to read to get updated ! All the best, Trond Saue -- ********************************************************************** * Trond Saue * Universitetet i Tromsoe Phone: +47/77645205 * Institutt for kjemi, MNF Fax : +47/77644765 * N-9037 TROMSOE, NORWAY * Check out the DIRAC home page: * http://dirac.chem.sdu.dk/ * WEB: http://www.chem.uit.no/KJEMI/TEOCHEM/trond.html * *********************************************************************** From chemistry-request@server.ccl.net Sat Jul 28 12:19:16 2001 Received: from web12701.mail.yahoo.com ([216.136.173.238]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6SGJF500300 for ; Sat, 28 Jul 2001 12:19:15 -0400 Message-ID: <20010728161915.46859.qmail@web12701.mail.yahoo.com> Received: from [65.6.48.45] by web12701.mail.yahoo.com; Sat, 28 Jul 2001 09:19:15 PDT Date: Sat, 28 Jul 2001 09:19:15 -0700 (PDT) From: water Miller Subject: Source code to analysis DNA melting curve To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, there, Is there any free source code available for DNA melting analysis? Prefer to the one that can give the results for melting propability at the whole temperature range, i.e. the curve. I notice that I can do it online from a few sites, but since I want to get the results for some modified DNA or RNA in order to compare with experiments, I wish I could change some part of the code. If anyone knows this kind of info, please let me know. Thanks a lot in advance. Water __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From chemistry-request@server.ccl.net Sat Jul 28 13:45:55 2001 Received: from embelia.wanadoo.fr ([193.252.19.161]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6SHjs503085 for ; Sat, 28 Jul 2001 13:45:54 -0400 Received: from andira.wanadoo.fr (193.252.19.152) by embelia.wanadoo.fr; 28 Jul 2001 19:45:48 +0200 Received: from cUDS85n31 (194.2.146.197) by andira.wanadoo.fr; 28 Jul 2001 19:45:47 +0200 DATE: 29 Jul 01 10:19:37 AM FROM: UI7Emy0N7@hongkong.com Message-ID: TO: -1-2-savon-phone-bill-@excite.com SUBJECT: RE: Cap your Long Distance Bill @ $69.95/mo. Never be surprised by your long distance bill again !! 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