From chemistry-request@server.ccl.net Wed Aug 8 05:30:48 2001 Received: from ns2.tudelft.nl ([130.161.180.65]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f789Umv31443 for ; Wed, 8 Aug 2001 05:30:48 -0400 Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost1.tudelft.nl (PMDF V6.0-24 #37171) with ESMTP id <0GHQ0093HT3C9S@mailhost1.tudelft.nl> for chemistry@ccl.net; Wed, 08 Aug 2001 11:30:48 +0200 (MET DST) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id f789UP108949 for ; Wed, 08 Aug 2001 11:30:25 +0200 (MEST) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Wed, 08 Aug 2001 11:29:59 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Wed, 08 Aug 2001 11:29:49 +0000 (MET-1MEST) Date: Wed, 08 Aug 2001 11:29:39 +0200 From: Stefan Bromley Subject: gaussian and Hirshfeld To: chemistry@ccl.net Message-id: <3B7122A5.21657.8CB4E09@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Goodmorning, We're interested in obtaining Hirshfeld charges from the output of Gaussian 98/Gamess-UK, does somebody know a package which can handle this. We've seen some mentioning of a package named "ESTAR" but the references were quite old. Thanks in advance, Stefan Bromley Martijn Zwijnenburg ________________________________________________________ Dr Stefan T. Bromley Laboratory of Applied Organic Chemistry and Catalysis DelftChemTech, Delft University of Technology Julianalaan 136, 2628 BL Delft The Netherlands Phone : + 31 1527 89418 e-mail : S.T.Bromley@tnw.tudelft.nl ________________________________________________________ From chemistry-request@server.ccl.net Wed Aug 8 05:34:00 2001 Received: from arrhenius.che.chalmers.se ([129.16.90.200]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f789Xxv06152 for ; Wed, 8 Aug 2001 05:34:00 -0400 Received: from arrhenius.che.chalmers.se (arrhenius.che.chalmers.se [129.16.90.200]) by arrhenius.che.chalmers.se (8.9.3/8.9.3) with ESMTP id LAA2067138 for ; Wed, 8 Aug 2001 11:24:27 +0200 (MDT) Date: Wed, 8 Aug 2001 11:24:27 +0200 From: Harald Svedung X-X-Sender: To: Subject: Re: CCL:beyond Verlet's algorithm In-Reply-To: <200108071245.OAA02595@chinon.cnrs-orleans.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII As a side note... I feel I've given it before ;-) For small systems like bimolecular collisions the variable time-step method with Gauss-Radau spaced substeps in: E. Everhart, in Dynamics of Comets: Their Origin and Evaluation, ed. A. Carusi and G. B. Valsecchi (Reidel, Dordrecht 1985) 185. was evaluated in: K. Bolton, S. Nordholm, J. Comp. Phys. 113 (1994) 320. and shows nice energy conservation and also keeps good track of rotational energy at a comparably light numerical load. I've always used it in my MD simulations of molecular collisions.... but then again I might have missed the original question here.. ;-) ... I don't think it will go to very large timesteps but try to stay within the frequencies. for all its worth :-) /Harald Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone:+46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden. www.che.chalmers.se/~svedung/welcome.html From chemistry-request@server.ccl.net Tue Aug 7 23:32:25 2001 Received: from hotmail.com ([64.4.37.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f783WPv11635 for ; Tue, 7 Aug 2001 23:32:25 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 7 Aug 2001 20:32:20 -0700 Received: from 133.11.92.210 by pv2fd.pav2.hotmail.msn.com with HTTP; Wed, 08 Aug 2001 03:32:19 GMT X-Originating-IP: [133.11.92.210] From: "tianxiao young" To: CHEMISTRY@ccl.net Subject: transition state Date: Wed, 08 Aug 2001 03:32:19 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 08 Aug 2001 03:32:20.0050 (UTC) FILETIME=[BABE5B20:01C11FBA] Dear CCLers, Do you know the best way to calculate the optimization transtion state using Gassian98? Your kind help is most appreciated. txyoung _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Wed Aug 8 16:27:39 2001 Received: from hydrogen.cen.brad.ac.uk ([143.53.238.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f78KRcv14422 for ; Wed, 8 Aug 2001 16:27:38 -0400 Received: from kestrel.cen.brad.ac.uk (kestrel.cen.brad.ac.uk [143.53.238.5]) by hydrogen.cen.brad.ac.uk (8.11.3/8.11.3) with ESMTP id f78KRcf03442 for ; Wed, 8 Aug 2001 21:27:38 +0100 (BST) Received: from v0g5l7 (max-132.dial.brad.ac.uk [143.53.239.132]) by kestrel.cen.brad.ac.uk (8.11.3/8.11.3) with SMTP id f78KRb012824 for ; Wed, 8 Aug 2001 21:27:37 +0100 (BST) Reply-To: From: "Vishal Chikhalia" To: Subject: Software for Tronac solution Calorimeter Date: Wed, 8 Aug 2001 21:22:43 +0100 Message-ID: <000001c12048$e317b380$84ef358f@v0g5l7> 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 CWS, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Does anyone have (or know the wherabouts of) software which will analyse the temperature vs time data that is produced from the Tronac isoperibol solution calorimeter (model no: 458). The software should be able to calculate the heat of solution (delta H) when the glass ampoule containing the product under test is broken, thereby releasing the test material into the solvent. Any form of software would be helpful either MS-DOS based or Windows. Have tried Tronac but they no longer produce any software!! Thanks, Vishal Chikhalia Drug Delivery Group Postgraduate Studies in Pharmaceutical Technology The School of Pharmacy University of Bradford Richmond Road Bradford BD7 1DP, U.K. Tel: 01274 232323 ext 4743 From chemistry-request@server.ccl.net Wed Aug 8 17:15:34 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f78LFXv16871 for ; Wed, 8 Aug 2001 17:15:33 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K6WDIE5F4E0019P8@trentu.ca> for chemistry@ccl.net; Wed, 8 Aug 2001 17:15:03 EDT Date: Wed, 08 Aug 2001 17:21:09 -0400 From: elewars Subject: Re: CCL:transition state To: chemistry@ccl.net Message-id: <3B71AD45.AF4414C4@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: re txyoung, TS calcs: First try to get a reasonable input geometry. I usually guess it (I find this almost always works), build it with an interacive molecule builder like GaussView or Spartan's builder, then do an AM1 or HF/3-21G TS optimization, then submit the AM1 or 3-21G TS structure to your ab initio or DFT calc. With Gaussian I usually use Opt(TS, CalcHFFC, NoEigenTest, MaxCycle=99) The CalcHHFC (calc Hartree-Fock Force constants) is to get a good Hessian if you are doing a correlated-level calc (e.g. MP2); for a HF-level calc omit it. NoEigenTest tells Gaussian not to check the eigenvalues of the Hessian as it goes along; Gaussian TS calcs always seem to fail if you omit NoEigenTest (at least G94 did). MaxCycle=99 is so a difficult job won't fail just because it ran out of optimization cycles. It may be helpful to get an AM1 or HF/3-21G TS using some other program, then feed the Cartesians into Gaussian. If you have problems guesssing a starting geom, Gaussian has algorithms for getting one from the reactant and product structures--look in help under optimization options. E. Lewars ================= tianxiao young wrote: > Dear CCLers, > > Do you know the best way to calculate the optimization transtion state using > Gassian98? Your kind help is most appreciated. > > txyoung > > _________________________________________________________________ > Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Aug 8 17:36:01 2001 Received: from cse.nd.edu (ako@[129.74.25.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f78La0v18892 for ; Wed, 8 Aug 2001 17:36:00 -0400 Received: from localhost (ako@localhost) by cse.nd.edu (8.11.2/8.11.2) with ESMTP id f78LZwA17420 for ; Wed, 8 Aug 2001 16:35:58 -0500 (EST) Date: Wed, 8 Aug 2001 16:35:58 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: CHARMM simulations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am new to molecular simulations. Does anyone know any good reference that shows how to run molecular simulations and particularly how to use CHARMM? Examples with explaination will help too. Any help is greatly appreciated. Thanks Alice