From chemistry-request@server.ccl.net Fri Jan 7 05:22:30 2000 Received: from info.cyf-kr.edu.pl (root@info.cyf-kr.edu.pl [149.156.4.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA30849 for ; Fri, 7 Jan 2000 05:22:28 -0500 Received: from kinga.cyf-kr.edu.pl (IDENT:4119@kinga.cyf-kr.edu.pl [149.156.2.32]) by info.cyf-kr.edu.pl (8.9.3/8.9.3) with ESMTP id LAA29368 for ; Fri, 7 Jan 2000 11:21:05 +0100 (MET) Received: (from mykrol@localhost) by kinga.cyf-kr.edu.pl (8.9.3/8.9.3) id LAA02960; Fri, 7 Jan 2000 11:21:01 +0100 (MET) Date: Fri, 7 Jan 2000 11:20:57 +0100 (MET) From: Marcin Krol To: chemistry@ccl.net Subject: MD simulations in water - Discover Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I'm trying to perform MD simulations of a protein in a water solution using Discover (MSI). First of all I simply soaked the molecule (standard 5A layer of waters) and began the simulation. However, after ~100 ps several water molecules 'evaporated' and the program stopped with an error message. So I tethered water molecules but it introduces artificial forces on the protein which limit its conformational flexibility. I'm also trying a PBC MD simulation but the CPU time of such calculations is huge. I think that the computationally cheapest and quite reasonable would be to run the simulation without explicit water molecules but to include solvation effects in solvation potentials or Generalized Born surface area (GB/SA). Is it possible to use GB/SA model in Discover? Are there any other solutions to the problem of evaporating waters during the MD simulation? Thanks in advance for your advice. Marcin Krol mykrol@cyf-kr.edu.pl From chemistry-request@server.ccl.net Fri Jan 7 06:42:49 2000 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA31175 for ; Fri, 7 Jan 2000 06:42:43 -0500 Received: from localhost (noronha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id JAA84043 for ; Fri, 7 Jan 2000 09:41:54 -0200 Date: Fri, 7 Jan 2000 09:41:54 -0200 (BDB) From: antonio luiz oliveira de noronha Reply-To: antonio luiz oliveira de noronha To: chemistry@ccl.net Subject: MOPAC2000 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would thank Drs. John MacKelvey and James J. P. Stewart for the help using the Miertus-Scrocco-Tomasi model in MOPAC2000. Best Regards Gentleman. ___________________________________________________________________ | | |Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br | |Medicinal Chemistry of Organotin Compounds | |NEQUIM - Medicinal Chemistry Group | |Chemistry Departament - DQ | |UFMG - Federal University of Minas Gerais - Brazil | |Av. Antonio Carlos, 6627 - Campus Pampulha | |CEP 31270-901 - Belo Horizonte - MG - Brazil | |VOICE +55 31 499 5765 - FAX +55 31 499 5700 | |___________________________________________________________________| From chemistry-request@server.ccl.net Fri Jan 7 13:10:02 2000 Received: from chem.chem.rochester.edu (root@chem.chem.rochester.edu [128.151.176.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00969 for ; Fri, 7 Jan 2000 13:10:01 -0500 Received: from chem.chem.rochester.edu (stc3.chem.rochester.edu [128.151.176.102]) by chem.chem.rochester.edu (8.8.5/8.8.5) with ESMTP id NAA12666 for ; Fri, 7 Jan 2000 13:08:15 -0500 (EST) Sender: jperl@chem.chem.rochester.edu Message-ID: <38762962.965939B4@chem.chem.rochester.edu> Date: Fri, 07 Jan 2000 12:58:58 -0500 From: Jerry Perlstein Organization: University of Rochester X-Mailer: Mozilla 4.5 [en] (X11; U; IRIX64 6.2 IP26) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCl:Boron MM parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Do any of you know of boron parameters for MM2 or MM3? JERRY -- ************** Jerry Perlstein Center for Photoinduced Charge Transfer Department of Chemistry University of Rochester Rochester,NY 14627-0216 Tel: (716)275-2511 FAX: (716)242-9485 perlstein@chem.chem.rochester.edu http://www.chem.rochester.edu/~stc/perlstein.html From chemistry-request@server.ccl.net Fri Jan 7 05:51:19 2000 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA31003 for ; Fri, 7 Jan 2000 05:51:18 -0500 Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id MAA10683 for ; Fri, 7 Jan 2000 12:49:12 +0200 (EET) Date: Fri, 7 Jan 2000 12:49:12 +0200 (EET) From: John Kerkines To: chemistry@ccl.net Subject: Re: CCL:Y2K molecule--correction In-Reply-To: <38754979.5406@trentu.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 6 Jan 2000, Errol Lewars wrote: > 2000 01 06 > > Re my message: > -------- > 2000 01 06 > > >Hello, > > >I hope CCLers will excuse me for mentioning, just before it ceases > >to be > >topical, the molecule Y2K (diytterbium potassium). See _Science_, > >17 > >December 1999, p. 2281. The authors conclude that its preparation > >is > >"unlikely to [represent an] explosive event" but that it "could be the > >material of the millenium." > > > E. Lewars > >=========== > > Sorry, Y is Yttrium, not Ytterbium (which is Yb). _My_ fault. Or maybe > my computer had a Y2k problem. > Hey is this thing superconducting? ;) ...because it reminds me of the story with the discovery of YBa2Cu3O7 ("accidentally" written as YbBa2.....). With Regards, John Kerkines From chemistry-request@server.ccl.net Fri Jan 7 16:58:32 2000 Received: from locke.howard.edu (locke.howard.edu [138.238.154.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA02340 for ; Fri, 7 Jan 2000 16:58:31 -0500 Received: from spollack.chem.howard.edu by locke.howard.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.0.1461.56) id CN5H025Q; Fri, 7 Jan 2000 16:57:37 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 7 Jan 2000 17:07:51 -0500 To: chemistry@ccl.net From: "Steven K. Pollack" Subject: More silliness When I was in Warren Hehre's group, we calculated the structure and energy for KrO3(6-) , Kryptonite. Isn't computational chemistry fun? Adamantium anyone? _______________________________________________________________________ Dr. Steven K. Pollack | Professor | Department of Chemistry | I notice that you are still Howard University | using polymers! 525 College St., NW | U.S.S. Enterprise Washington, DC 20059 | - Lt. Commander Montgomery Scott ======================================================================= http://www.chem.howard.edu/~spollack/ | spollack@fac.howard.edu | (202)-806-6892 | (202)-806-4250(FAX) | ========================================== From chemistry-request@server.ccl.net Fri Jan 7 17:17:47 2000 Received: from igor.wag.caltech.edu (igor.wag.caltech.edu [131.215.33.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA02458 for ; Fri, 7 Jan 2000 17:17:47 -0500 Received: from wag.caltech.edu (octane2 [131.215.33.125]) by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id OAA141222 for ; Fri, 7 Jan 2000 14:16:48 -0800 (PST) Sender: rpm@wag.caltech.edu Message-ID: <387665CF.C75457F8@wag.caltech.edu> Date: Fri, 07 Jan 2000 14:16:47 -0800 From: "Richard P. Muller" X-Mailer: Mozilla 4.6 [en] (X11; U; IRIX64 6.4 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Pekeris Technique for 2-electron Atoms References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I'm currently working on 2-electron atoms using Pekeris' approach (see Phys Rev 112, 1649 (1958) and Phys Rev 115, 1216 (1959)). I believe that Equation 22 of the 1958 paper has an error in it, because the results don't agree with the special case results for the 7x7 case that Pekeris puts on the following page of that paper. I've checked my work several times, but there still appears to be something wrong. I looked for, but did not find, a published errata for this paper, which concerns me, since they've certainly had time to get a correction out, so I could be doing something dumb. Has anyone else worked through this paper? If so, could they offer me any help. Thanks very much in advance. Rick Muller From chemistry-request@server.ccl.net Wed Jan 5 09:25:53 2000 Received: from bclcl1.im.battelle.org (bclcl1.im.battelle.org [131.167.1.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA17358 for ; Wed, 5 Jan 2000 09:25:53 -0500 Received: from ns-bco-mse1.im.battelle.org ([131.167.1.166]) by BCLCL1 (PMDF V5.1-10 #U2779) with ESMTP id <01JKC7C9YWB48WW2VE@BCLCL1> for CHEMISTRY@ccl.net; Wed, 5 Jan 2000 08:15:06 EST Received: by ns-bco-mse1.im.battelle.org with Internet Mail Service (5.5.2448.0) id ; Wed, 05 Jan 2000 08:15:06 -0500 Content-return: allowed Date: Wed, 05 Jan 2000 08:15:01 -0500 From: "Risser, Steven M" Subject: Solid state themodynamics To: "'CHEMISTRY@ccl.net'" Message-id: <8D6D98F05334D1118BE600A0C96E9612023AEFA6@ns-bco-mse4.im.battelle.org> X-Mailer: Internet Mail Service (5.5.2448.0) Hi all, I am interested in calculating the tyhermodynamic properties (particularly heat capacity) of a solid. I would appreciate any suggestions on methods, useful software, etc... I am already familiar with the standard methods of deriving the molecular thermo properties from molecules, and was hoping for a similar approach for solids. Thanks in advance Steve ****************************************************** Dr. Steven M. Risser Principal Research Scientist Core Technology Battelle Memorial Institute rissers@battelle.org 614-424-3715 614-424-7479 (FAX) ******************************************************