From weishi@umich.edu Tue Feb 24 19:10:19 2004 Return-Path: Date: Tue, 24 Feb 2004 19:11:23 -0500 (EST) From: Wei Shi X-X-Sender: weishi!at!zektor.gpcc.itd.umich.edu To: Rick Venable cc: chemistry!at!ccl.net Subject: ENERGY CHANGE TOLERANCE EXCEEDED in CHARMM In-Reply-To: Message-ID: References: MIME-Version: 1.0 Hi, Rick, I am sorry to send you an email again for my question. However, I think your expert knowledge about CHARMm is very helpful to me. I am performing a NVE simulation using CHARMM. After some steps of simulations, the program exited saying that ENERGY CHANGE TOLERANCE EXCEEDED. How can I avoid this kind of problem? In the NVE MD simulations, if one scales the temperature periodically in the equilibration phase, one should expect the ENERGy to change, right? Anyway, it seems strange to me why the code checks the energy change. >From my experience for small molecules, one need not to check the energy change in the NVE MD simulations. Thanks very much for your help, Wei Shi From chemistry-request@ccl.net Wed Feb 25 09:14:54 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1PEEqcS023764; Wed, 25 Feb 2004 09:14:53 -0500 To: bmbmre..at..bmb.leeds.ac.uk Cc: chemistry..at..ccl.net, "Computational Chemistry List" Subject: Re: CCL:software for lead optimisation? MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: Andras.Borosy..at..givaudan.com Date: Wed, 25 Feb 2004 15:15:52 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.07a |May 14, 2001) at 25/02/2004 15:16:12, Serialize complete at 25/02/2004 15:16:12 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.3 required=7.0 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i1PEEscS023774 Dear Monika,, I wonder that you found free software for such a task. However either Leapfrog of Tripos or Sprout (http://www.simbiosys.ca/products/sprout_sheet.html) of Simbiosys or Jchem (http://www.jchem.com/index.html) must not be expensive for academic users. Best wishes, Andras Borosy PhD Computational Chemist Givaudan Schweiz AG Fragrance Research Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy..at..givaudan.com Monika Rella Sent by: "Computational Chemistry List" 13.02.2004 18:23 To: cc: Subject: CCL:software for lead optimisation? Hello CCLers! Can anyone please advise me about free software for lead optimisation? I'm thinking about a tool like LUDI or Sybyl's RACHEL module that performs "automated combinatorial optimization of lead compounds by systematically derivatizing user-defined sites on the ligand". Any suggestions wellcome! Regards, Monika -- ****************************************************************************************** Monika Rella PhD Bioinformatics Research Student School of Biochemistry and Molecular Biology University of Leeds, LS2 9JT, UK E-mail: bmbmre..at..bmb.leeds.ac.uk Tel: +44 (0) 113 343 4447 ***************************************************************************************** -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY..at..ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow..at..nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Feb 25 09:14:40 2004 Received: from mprelay.uc.edu (mprelay.uc.edu [129.137.3.48]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1PEEdcS023737 for >ccl.net>; Wed, 25 Feb 2004 09:14:39 -0500 Received: from mirapoint.uc.edu (mirapoint.uc.edu [10.23.4.254]) by mprelay.uc.edu (Mirapoint Messaging Server MOS 3.3.8-GR) with ESMTP id ARZ18476; Wed, 25 Feb 2004 09:15:45 -0500 (EST) Received: from 10.39.6.48 by mirapoint.uc.edu (Mirapoint Messaging Server MOS 3.3.8-GR) with HTTP/1.1; Wed, 25 Feb 2004 09:15:45 -0500 Date: Wed, 25 Feb 2004 09:15:45 -0500 From: Chi-Yuan Chen >email.uc.edu> Subject: COMPASS v.s. ESFF !! To: Computational Chemistry List>ccl.net> X-Mailer: Webmail Mirapoint Direct 3.3.8-GR MIME-Version: 1.0 Message-Id: >mirapoint.uc.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.2 required=7.0 tests=DEAR_SOMETHING autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Sirs: Does anyone know the critical differences between COMPASS and ESFF force field ?? And will these affect the limitation of each force field ?? thanks Chi-Yuan Chen Graduate Student Center for Computer-Aided Molecular Design Department of Chemical and Materials Engineering University of Cincinnati Cincinnati, Ohio 45221-0171 Email: chenca<>email.uc.edu From chemistry-request@ccl.net Wed Feb 25 12:09:54 2004 Received: from electra.cc.umanitoba.ca (electra.cc.umanitoba.ca [130.179.16.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i1PH9rcS031651 for ; Wed, 25 Feb 2004 12:09:53 -0500 Received: from cc.umanitoba.ca (net118.chem.umanitoba.ca [130.179.49.38]) by electra.cc.umanitoba.ca (8.12.10/8.12.10) with ESMTP id i1PHAwUj003900; Wed, 25 Feb 2004 11:10:59 -0600 (CST) Date: Wed, 25 Feb 2004 11:14:06 -0600 Subject: summary: periodic boundary conditions Content-Type: multipart/alternative; boundary=Apple-Mail-2-637798664 Mime-Version: 1.0 (Apple Message framework v553) Cc: "H. Georg Schreckenbach" To: chemistry.-at-.ccl.net From: "H. Georg Schreckenbach" Message-Id: <047A5DC4-67B6-11D8-A028-000A9593094A.-at-.cc.umanitoba.ca> X-Mailer: Apple Mail (2.553) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --Apple-Mail-2-637798664 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Dear CCL, as promised, here is my summary for the recent question. As usual, I got the kind of replies that I was looking for -- thank you very much! Best regards, Georg Schreckenbach ============================= Original question: Date: Thu Feb 19, 2004 1:18:03 PM America/Winnipeg Subject: periodic boundary conditions Dear CCL, I am looking for recommendations regarding literature about band-structure calculations. Specifically, we are coming from the "molecular electronic structure" background, and we want to branch out into extending some of our methods, applications and ideas into extended structures that require periodic boundary conditions. For that, we are looking for introductory material that explains to us the basic concepts etc. To give an example, we are thinking about questions such as, what is the equivalent of the total energy expressions that are the basis for most molecular methods? I appreciate your help! Please reply directly to me because I am not currently subscribed to the list. I will definitely post a summary. ============================= Replies: From: enb.-at-.rice.edu A lot of this stuff has been added to Gaussian recently, which is very similar, i.e. molecular QM being extended to PBC. A great series of papers (which provide a good set of background reference as well) are by Konstantin N. Kudin and Gustavo E. Scuseria. They've published primarily in Chem. Phys. Lett., J. Chem. Phys., and Phys. Rev. B. A science citation search will be much more comprehensive of their publications, but I think they're papers give the simplest beginning. Ed Brothers. From: Szieberth Denes Some papers I have found useful: a "for beginners" one: Gillan MJ The virtual matter laboratory CONTEMP PHYS 38 (2): 115-130 MAR-APR 1997 and two "serious" ones: Jones & Gunnarsson Rev Mod Phys 91 (1989) 689 M. Payne et al Rev Mod Phys 64 (1992) 1045 cheers, dino From: "Dr. Alexander Hofmann" Hi Georg, try R. Hoffmann: Solids and Surfaces: A chemist's view ... Elliot: The physics and chemistry of surfaces More technical and plane wave related @article{a:Payne1, author="Payne, M. C. and Teter, M. P. and Allan, D. C. and Arias, T. A. and Joannopoulos, J. D.", title="Iterative minimization techniques for {{\em ab initio}} total-energy calculations: molecular dynamics and conjugate gradients", journal=revmodphys, year="1992", volume="64", number="4", pages="1045--1097"} or for LCAO Pisani (ed.) Quantum-Mechanical Ab-initio Calculation of the Properties of Crystalline Materials (Lecture Notes in Chemistry Vol. 67), Springer Hth, Alex Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie, Arbeitsgruppe Quantenchemie Post: Unter den Linden 6, 10099 Berlin Visitors: Brook-Taylor-Strasse 2, 12489 Berlin ah.-at-.chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 From: Konstantin Kudin Dear Georg Check out our paper describing how PBC is implemented in G03: K.N.Kudin and G.E.Scuseria, PRB,61,16440(2000). There, we tried to keep things as close as possible to the way they are done in molecular quantum chemistry programs. Regards, Konstantin -- Dr. H. Georg Schreckenbach Department of Chemistry, University of Manitoba Winnipeg, MB, R3T 2N2, Canada phone: (+204) 474-6261 FAX: (+204) 474-7608 http://home.cc.umanitoba.ca/~schrecke/ --Apple-Mail-2-637798664 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Dear CCL, as promised, here is my summary for the recent question. As usual, I got the kind of replies that I was looking for -- thank you very much! Best regards, Georg Schreckenbach ============================= Original question: Date: Thu Feb 19, 2004 1:18:03 PM America/Winnipeg Subject: periodic boundary conditions Dear CCL, I am looking for recommendations regarding literature about band-structure calculations. Specifically, we are coming from the "molecular electronic structure" background, and we want to branch out into extending some of our methods, applications and ideas into extended structures that require periodic boundary conditions. For that, we are looking for introductory material that explains to us the basic concepts etc. To give an example, we are thinking about questions such as, what is the equivalent of the total energy expressions that are the basis for most molecular methods? I appreciate your help! Please reply directly to me because I am not currently subscribed to the list. I will definitely post a summary. ============================= Replies: From: enb.-at-.rice.edu A lot of this stuff has been added to Gaussian recently, which is very similar, i.e. molecular QM being extended to PBC. A great series of papers (which provide a good set of background reference as well) are by Konstantin N. Kudin and Gustavo E. Scuseria. They've published primarily in Chem. Phys. Lett., J. Chem. Phys., and Phys. Rev. B. A science citation search will be much more comprehensive of their publications, but I think they're papers give the simplest beginning. Ed Brothers. From: Szieberth Denes < Some papers I have found useful: a "for beginners" one: Gillan MJ The virtual matter laboratory CONTEMP PHYS 38 (2): 115-130 MAR-APR 1997 and two "serious" ones: Jones & Gunnarsson Rev Mod Phys 91 (1989) 689 M. Payne et al Rev Mod Phys 64 (1992) 1045 cheers, dino From: "Dr. Alexander Hofmann" < Hi Georg, try R. Hoffmann: Solids and Surfaces: A chemist's view ... Elliot: The physics and chemistry of surfaces More technical and plane wave related @article{a:Payne1, author="Payne, M. C. and Teter, M. P. and Allan, D. C. and Arias, T. A. and Joannopoulos, J. D.", title="Iterative minimization techniques for {{\em ab initio}} total-energy calculations: molecular dynamics and conjugate gradients", journal=revmodphys, year="1992", volume="64", number="4", pages="1045--1097"} or for LCAO Pisani (ed.) Quantum-Mechanical Ab-initio Calculation of the Properties of Crystalline Materials (Lecture Notes in Chemistry Vol. 67), Springer Hth, Alex Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie, Arbeitsgruppe Quantenchemie Post: Unter den Linden 6, 10099 Berlin Visitors: Brook-Taylor-Strasse 2, 12489 Berlin ah.-at-.chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 From: Konstantin Kudin < Dear Georg Check out our paper describing how PBC is implemented in G03: K.N.Kudin and G.E.Scuseria, PRB,61,16440(2000). There, we tried to keep things as close as possible to the way they are done in molecular quantum chemistry programs. Regards, Konstantin -- Dr. H. Georg Schreckenbach Department of Chemistry, University of Manitoba Winnipeg, MB, R3T 2N2, Canada phone: (+204) 474-6261 FAX: (+204) 474-7608 http://home.cc.umanitoba.ca/~schrecke/ --Apple-Mail-2-637798664-- Return-Path: Message-Id: <6.0.3.0.0.20040225183910.01eda588@133.164.253.30> Date: Wed, 25 Feb 2004 18:41:37 -0800 To: chemistry:at:ccl.net From: David Gallagher Subject: CCL: CAChe Site Licenses for Chemistry & Biochemistry CAChe Academic Annual Site Licenses for Chemistry & Biochemistry now includes UNLIMITED licenses for students & faculty, at home & Lab ---------------------------------------------------------------------------- + New 6.1.1 Release for Windows http://www.cachesoftware.com/pdfs/CAChe_6.1_Datasheet.pdf + Free "Teaching with CAChe" instructors workbook http://www.cachesoftware.com/cache/education.shtml + New automated reaction path movie feature http://www.cachesoftware.com/ + Automatically run Gaussian from CAChe + Protein analysis & sequence alignment tools + New automated ligand-protein docking (Fastdock) + For Windows and Macintosh + Runs on 3D Auto-stereo Sharp laptop & other stereo HW + From $1,000 per year (unlimited licenses) --------------------------------------------------------------------------- The No. 1 Computer-Aided Chemistry Software for Teaching --------------------------------------------------------------------------- 10% early-bird discount for orders placed before March 31st, 2004 (renewals & new orders) For further information email sales:at:cachesoftware.com, call 1 503 746 3602, or visit http://www.CACheSoftware.com