From chemistry-request@server.ccl.net Thu Nov 8 04:44:13 2001 Received: from mail.crs4.it ([156.148.1.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA89iCB02283 for ; Thu, 8 Nov 2001 04:44:13 -0500 Received: from mercurio.crs4.it (mercurio.crs4.it [156.148.4.11]) by mail.crs4.it (Postfix) with SMTP id B449110F5 for ; Thu, 8 Nov 2001 10:57:47 +0100 (MET) Sender: ronzitti@crs4.it Message-ID: <3BEA565F.5452@crs4.it> Date: Thu, 08 Nov 2001 10:54:39 +0100 From: Cristina Ronzitti X-Mailer: Mozilla 3.01Gold (X11; I; HP-UX B.10.20 9000/778) MIME-Version: 1.0 To: chemistry@ccl.net Subject: deltat choice (help request) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone, I'm beginning a molecular dynamics simulation for my final thesis and I don't know how to find the suitable delta t. Any suggestion ? I know it should be about 1 fs but I tried to use this value and lesser values and I got as results nanq values or segmentation fault error. My system has the following kind of bonds: C-F, C-S, S-O , H-O . Thanks in advance for every suggestions, Cristina ronzitti@crs4.it -- ________________________________________________________________________ Cristina Ronzitti Degree: final-year in chemistry Chemical Processes and Material Modelling Area - Fuel Cells Project CRS4 - VI strada ovest - Z.I. - Macchiareddu - UTA - Cagliari _____________________________________________________________________ From chemistry-request@server.ccl.net Thu Nov 8 14:02:37 2001 Received: from mhub16.lvs.dupont.com ([52.128.30.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA8J2bB12188 for ; Thu, 8 Nov 2001 14:02:37 -0500 Received: from mhub3.lvs.dupont.com by mhub16.lvs.dupont.com with ESMTP for chemistry@ccl.net; Thu, 8 Nov 2001 14:02:30 -0500 Received: from CDCLN05.LVS.DUPONT.COM by mhub3.lvs.dupont.com with ESMTP for chemistry@ccl.net; Thu, 8 Nov 2001 14:02:17 -0500 Subject: Code for solvinging 1D rotational Schrodinger equation To: chemistry@ccl.net From: "Robert L Waterland" Date: Thu, 8 Nov 2001 14:02:02 -0500 Message-Id: X-MIMETrack: Serialize by Router on CDCLNMH1/DuPont_MHUB(Release 5.0.8 |June 18, 2001) at 11/08/2001 02:02:17 PM MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does anyone know where I can obtain code for solving the 1D rotational Schrodinger equation given a user specified potential V(theta). I need to do this to estimate the contribution to the entropy for internal rotation and find that the famous tables in Pitzer's papers are not sufficient for the cases I'm studying. Thanks, Rob Waterland DuPont email: Robert.L.Waterland@usa.dupont.com From chemistry-request@server.ccl.net Thu Nov 8 15:08:53 2001 Received: from mailhub.appstate.edu ([152.10.1.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA8K8qB13864 for ; Thu, 8 Nov 2001 15:08:52 -0500 Received: from ws2.appstate.edu (SYSTEM@ws2.appstate.edu [152.10.1.41]) by mailhub.appstate.edu (8.11.0/8.10.1) with ESMTP id fA8JoJl26060 for ; Thu, 8 Nov 2001 14:50:19 -0500 Received: from CONVERSION-DAEMON.appstate.edu by appstate.edu (PMDF V6.0-025 #41615) id <01KAGRN5AUM89EXEEY@appstate.edu> for CHEMISTRY@ccl.net; Thu, 08 Nov 2001 15:08:44 -0400 (EDT) Received: from kohn.appstate.edu (cohn.chem.appstate.edu [152.10.114.100]) by appstate.edu (PMDF V6.0-025 #41615) with ESMTP id <01KAGRML5NPI9R4PH5@appstate.edu> for CHEMISTRY@ccl.net; Thu, 08 Nov 2001 15:00:46 -0400 (EDT) Date: Thu, 08 Nov 2001 15:01:18 -0500 From: Steve Williams Subject: anharmonic oscillator wavefunctions X-Sender: willsd@imap.appstate.edu To: CHEMISTRY@ccl.net Message-id: <5.1.0.14.0.20011108145055.00b135d8@imap.appstate.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; charset=us-ascii; format=flowed I have a colleague who is interested in computing Franck-Condon factors, for which he needs anharmonic oscillator wavefunctions. I think that I can provide him with some good potentials (he is interested in first row diatomics) from something like ccsd(t) scans with one of the aug-cc basis sets. My plan was to fit the resulting potential to a Morse function, then get the anharmonic wavefunctions by diagonalizing the anharmonic (Morse) Hamiltonian on a basis of harmonic oscillator functions. I am not certain that this fit will be good enough, particularly in the repulsive regime. I have poked about in the literature some, but have not yet found the definitive "best" way to do this. I suspect there are some ccl users who know about getting good quality vibrational wavefunctions from ab initio potentials, and there may be some existing code out there to help solve this problem. I'd appreciate any suggestions, pointers to papers that I have overlooked, or codes. I'll post a summary on this topic soon. Steve Williams Steve Williams A. R. Smith Department of Chemistry Appalachian State University Boone, NC 28608 USA 828-262-2965 From chemistry-request@server.ccl.net Thu Nov 8 16:37:25 2001 Received: from eden.rutgers.edu ([165.230.180.177]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA8LbPB15870 for ; Thu, 8 Nov 2001 16:37:25 -0500 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by eden.rutgers.edu (Postfix) with ESMTP id B9D519F806 for ; Thu, 8 Nov 2001 16:37:23 -0500 (EST) Message-ID: <3BEAFDC7.7E5A030A@eden.rutgers.edu> Date: Thu, 08 Nov 2001 16:48:55 -0500 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: (no subject) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In response to my recent request for reviews of water models, I want to thank Dr. Boyd for suggesting:Wallqvist and Mountain, Reviews in Computational Chemistry Vol 13, 1999. pp 183-247. I also want toi thank everyone else who replied: I generally printout replies in order to read them, and then summarize. I regret that these were accidentally recycled before I summarized (although I did order the suggested papers). I will not let that happen again. Mary O'Connor Rutgers University New Brunswick, NJ From chemistry-request@server.ccl.net Thu Nov 8 16:51:54 2001 Received: from eden.rutgers.edu ([165.230.180.177]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA8LpsB16171 for ; Thu, 8 Nov 2001 16:51:54 -0500 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by eden.rutgers.edu (Postfix) with ESMTP id 91CA29F806 for ; Thu, 8 Nov 2001 16:51:52 -0500 (EST) Message-ID: <3BEB012C.DDFD7075@eden.rutgers.edu> Date: Thu, 08 Nov 2001 17:03:24 -0500 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: reviews of water models Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I looked under another pile of papers and found the replies to the query for reviews of water models: Martin Chaplin reviews water models at:www.sbu.ac.uk/water/models.html Chandra Verma:"Structure and Dynamics of the TIP3P,SPC, and SPC/E water models at 298K" P.Mark and L.Nilsson .JPCA(2001 Casey Kelly:comp.chem.umn.edu/solvation/solref.html Ivan Tubert:"A five-side model for liquid water and the reproduction of the density anomaly by rigid,non-polarizable potential functions". Mahoney and Jorgenson J. Chem. Phys. 112 (20) 8910-8922 (2000). Again, thank you all. I hope this upgrades me from total moron to at least half-wit. Mary O'Connor Rutgers University New Brunswick, NJ From chemistry-request@server.ccl.net Thu Nov 8 17:13:49 2001 Received: from eden.rutgers.edu ([165.230.180.158]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA8MDmB16702 for ; Thu, 8 Nov 2001 17:13:48 -0500 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by eden.rutgers.edu (Postfix) with ESMTP id 6586AA29B1 for ; Thu, 8 Nov 2001 17:13:47 -0500 (EST) Message-ID: <3BEB064F.664292E2@eden.rutgers.edu> Date: Thu, 08 Nov 2001 17:25:19 -0500 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: re: HOMO/LUMO values from Gaussian98 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have values for the HOMO/LUMO of a successively protonated heterocyclic molecule. I know that the negative of the eigenvalue for an orbital,by Koopman's theorem, is the ionozation potential. I know that the coefficients indicate how much each atomic orbital contributes to the molecular orbital. However, being new to this, can anyone help me as to what else I can glean from such data? The Foresman and Frisch book does not go in to much detail. Thank-you. Mary O'Connor Rutgers University New Brunswick,NJ From chemistry-request@server.ccl.net Thu Nov 8 20:08:30 2001 Received: from janus.hosting4u.net ([209.15.2.37]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fA918UB24242 for ; Thu, 8 Nov 2001 20:08:30 -0500 Received: (qmail 25507 invoked from network); 9 Nov 2001 01:08:29 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 9 Nov 2001 01:08:29 -0000 Received: from yersina ([211.26.1.3]) by proinformatix.com ; Thu, 08 Nov 2001 19:08:23 -0600 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: Animations Date: Fri, 9 Nov 2001 11:13:45 -0800 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Dear all, check out www.proinformatix.com/movies.html to view the most recent movies I have made of proteins in action. All these are in Quicktime format, and quite small. Cheers Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/