From chemistry-request@server.ccl.net Thu Jan 4 03:36:14 2001 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA07576 for ; Thu, 4 Jan 2001 03:36:11 -0500 Received: from fenII-121 (fenII-121.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with SMTP id KAA24873 for ; Thu, 4 Jan 2001 10:35:44 +0200 (EET) Message-Id: <3.0.2.32.20010104103521.006a5ee0@century.fen.bilkent.edu.tr> X-Sender: salzner@century.fen.bilkent.edu.tr X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Thu, 04 Jan 2001 10:35:21 +0200 To: chemistry@ccl.net From: Ulrike Salzner Subject: running G98 parallel Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I am using a SUN Ultrasparc with 12 processors, 3GB of memory and 21GB of disk space to run G98. Usually I am requesting 6 processors, since there is no speed up by adding more processors. With large jobs I am getting messages like the one below: 1144 basis functions 1808 primitive gaussians 181 alpha electrons 181 beta electrons nuclear repulsion energy 4338.5221150204 Hartrees. PrsmSu: requested number of processors reduced to: 3 ShMem 1 Linda. 4 Symmetry operations used in ECPInt. ECPInt: NShTT= 34980 NPrTT= 100852 LenC2= 14488 LenP2D= 30980. LDataN: DoStor=F MaxTD1= 4 Len= 56 LDataN: DoStor=T MaxTD1= 4 Len= 56 Number of processors reduced to 1 by ecpmxn. Projected Huckel Guess. It looks to me like the number of processors reduces because there is not enough memory. After requesting 16 Mio words of memory, the number of processors reduces to 3. I am not sure how far I can go, since G98 gets very slow when more memory is requested than is available. If a normal job would use 8 Mio words, should this be multiplied by the number of processors? How are these machines distributing the memory? Most of the time I am the only user on the machine but what happens if a second user starts a job that needs a lot of memory? Also, if two jobs are running, would it be better to use 12 processors and let the machine decide what to do or is it better to give 6 processors to each job? Is there a rule of thumb as to what works best? Thanks in advance and happy New Year, Uli Salzner Dr. Ulrike Salzner e-mail:salzner@fen.bilkent.edu.tr Associate Professor Tel.: 90-312-290-2122 Department of Chemistry Fax.: 90-312-266-5097 Bilkent University 06533 Bilkent, Ankara,Turkey From chemistry-request@server.ccl.net Wed Jan 3 18:04:30 2001 Received: from catios.udea.edu.co (catios.udea.edu.co [200.24.20.180]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA05739 for ; Wed, 3 Jan 2001 18:04:27 -0500 Received: from labqca151 (prof-ccias-exac1-052.udea.edu.co [200.24.17.75]) by catios.udea.edu.co (8.9.3/8.9.3) with SMTP id RAA07600 for ; Wed, 3 Jan 2001 17:56:16 -0500 Message-ID: <001101c075d9$a8f119e0$4b1118c8@udea.edu.co> From: "Alejandro Montoya" To: "CCL list" Subject: On tendencies in Computational chemistry Date: Wed, 3 Jan 2001 18:05:26 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000E_01C075AF.BFE11620" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_000E_01C075AF.BFE11620 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello CCL users, =20 As far as I know, in the book "Reviews in computational chemistry" = there is information on trends in computational chemistry and how it is = spread all over the world. =20 =20 I would be glad if someone may let me know if there is updated = information on this topic and where can I look for it. Is there a web = page where this information is updated? =20 Thanks a lot. Alejandro =20 ______________________________ ------=_NextPart_000_000E_01C075AF.BFE11620 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello CCL users,
 
As far as I know, in the book "Reviews = in=20 computational chemistry"  there is information on trends in=20 computational chemistry and how it is spread all over the=20 world.  
 
I would be glad if = someone may let=20 me know if there is updated information on this topic and = where can I=20 look for it.  Is there a web page where this information is=20 updated?
 
Thanks a lot.
Alejandro   
______________________________
------=_NextPart_000_000E_01C075AF.BFE11620-- From chemistry-request@server.ccl.net Thu Jan 4 10:29:24 2001 Received: from asp.biogeo.uw.edu.pl (root@asp.biogeo.uw.edu.pl [212.87.8.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA10442 for ; Thu, 4 Jan 2001 10:29:23 -0500 Received: (from grzesb@localhost) by asp.biogeo.uw.edu.pl (8.9.3/8.9.3) id QAA09981 for chemistry@ccl.net; Thu, 4 Jan 2001 16:30:03 +0100 Date: Thu, 4 Jan 2001 16:30:03 +0100 From: Grzegorz Bakalarski To: chemistry@ccl.net Subject: vdW parameters Message-ID: <20010104163003.A9930@asp.biogeo.uw.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2i Dear All, Recently I analyzed vdW parameters in different force fields (sybyl, few flavors from MSI, Charmm, MM3 etc) and I noticed that the parameters differ substantially! In crystallografer community the most popular are Bondi vdW radii and they are in most cases completely different from those used in forcefields. The only exception is sybyl forcefield, but here also parameter for H atom is 1.5 A (instead of 1.2 A) which gives 0.6A difference for H-H interaction. My question is: what is origin of these (huge) differences ? Physical origin of the vdW is known and should not change from forcefiled to forcefield ... In a case of overlapping H-H pair a repulsive force calculated using sybyl vdW radii is substantial, (e.g. if distance is 2.5A) but using Bondi's radii the force is small and even attracting Thanks in advance for any comments Regards, G.Bakalarski From chemistry-request@server.ccl.net Thu Jan 4 11:18:16 2001 Received: from coyote.iupui.edu (coyote.iupui.edu [134.68.220.82]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA10695 for ; Thu, 4 Jan 2001 11:18:16 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by coyote.iupui.edu (8.9.3/8.9.3/IUPUIPO.20001219) with SMTP id LAA24108; Thu, 4 Jan 2001 11:17:35 -0500 (EST) Message-ID: Date: 4 Jan 2001 11:37:12 -0500 From: "Boyd" Subject: re: On tendencies... To: "Montoya, Alejandro" , "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hello Alejandro, I presume you are referring to the material that was in the preface of Vol. 9 (1996) of "Reviews in computational chemistry. The data showed the use of computational chemistry around the world. As far as I know, a similar study with more recent data has not been done. Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (for the ACS COMP division) http://chem.iupui.edu/rcc/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Tel. 317-274-6891, Fax 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Thu Jan 4 12:51:40 2001 Received: from smtp10.atl.mindspring.net (smtp10.atl.mindspring.net [207.69.200.246]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA11177 for ; Thu, 4 Jan 2001 12:51:40 -0500 Received: from smui05.slb.mindspring.net (smui05.slb.mindspring.net [199.174.114.91]) by smtp10.atl.mindspring.net (8.9.3/8.8.5) with ESMTP id MAA14672 for ; Thu, 4 Jan 2001 12:51:23 -0500 (EST) Received: by smui05.slb.mindspring.net id MAA0000009090; Thu, 4 Jan 2001 12:51:22 -0500 (EST) Date: Thu, 04 Jan 2001 12:51:22 -0500 From: Dave Young To: chemistry@ccl.net Reply-To: dave.young@springmail.com Subject: David Young's web site Sender: dave.young@springmail.com Message-ID: X-Originating-IP: 209.196.125.101 Hi, A couple weeks ago, there was some discussion on the list about my "Chemical Topics" web site. As mentioned previously, it was removed from the Auburn University server when I took a job with Cytoclonal Pharmaceutics in Dallas. The CCL documents archive has now been updated with the most recent version of these pages. I know that they have been mirrored other places; some with my permission and most without. However, the CCL is the only place that I am taking an active role in keeping the collection updated. This collection has also been expanded into a book titled "Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems" which will be available from John Wiley & Sons in a few months. I have noted several cases in the past where public domain information or software mysteriously disappeared when a commercial version became available, but I don't personally agree with this practice. The folks at Wiley were very good about agreeing to this, so I can keep and expand the web page collection on the CCL permanently. Unfortunately, my new job has me spending more time writing patents than web pages. I hope you get some use from these. Dave Young dave.young@springmail.com From chemistry-request@server.ccl.net Thu Jan 4 12:52:56 2001 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA11189 for ; Thu, 4 Jan 2001 12:52:56 -0500 Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP for id f04HqgY03222 (8.11.1/3.14); Thu, 4 Jan 2001 18:52:42 +0100 (MET) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost for chemistry@ccl.net id SAA27574 (8.8.8/3.1); Thu, 4 Jan 2001 18:52:41 +0100 (MET) Date: Thu, 4 Jan 2001 18:52:41 +0100 (MET) Message-Id: <200101041752.SAA27574@studs3.sci.kun.nl> To: chemistry@ccl.net It is our pleasure to announce the release 0.8 of JChemPaint. JChemPaint is a Java 2 program for drawing 2D chemical structures like those found in most chemistry textbooks. The program is developed as an Open Source Project and released under GNU Lesser General Public License (LGPL). The code should have beta quality since we are approaching release 1.0 JChemPaint is developed by Christop Steinbeck, Egon Willighagen, Martin Schild, Stefan Krause and others and hosted by SourceForge (http://jchempaint.sourceforge.net and http://sourceforge.net/projects/jchempaint) New features in version 0.8: - Clean up of multiple molecules in one document now works. - Colouring of substructures. - Now possible to assign charges to atoms. - Drawing of implicit hydrogens. - Structures can now be accompanied with some properties: Generator, Software, CAS-number and generation date. - Insert SMILES functionality (By entering them in a pop-up window) - Help functionality with complete user manual. - Greatly improved website - Export filter for SVG. - Print capabilities. - Download structures from the internet (over 200.000 structures) For those who just want to run the program, I recommend the binary version: Binaries: ZIP format: http://download.sourceforge.net/jchempaint/JChemPaint-0.8.zip TGZ format: http://download.sourceforge.net/jchempaint/jchempaint-0.8.tar.gz The source code can be checkout from CVS with: cvs -d:pserver:anonymous@cvs.JChemPaint.sourceforge.net:/cvsroot/jchempaint login cvs -z3 -d:pserver:anonymous@cvs.JChemPaint.sourceforge.net:/cvsroot/jchempaint co JChemPaint Just click ENTER when it asks for the password. More information as well as a download option can be found on http://jchempaint.sourceforge.net. JChemPaint is associated with the OpenScience project (www.openscience.org) and the 3D molecular viewer Jmol (http://www.openscience.org/jmol/), both initiated by Dan Gezelter at the University of Notre Dame (http://www.nd.edu/~gezelter/) We would be happy to get some feedback from people who have downloaded and tested the program. Also people who want to join the development of JChemPaint or want to contribute code are welcomed. From chemistry-request@server.ccl.net Thu Jan 4 13:20:20 2001 Received: from popserver.chealth.com (smtpmail.cambridgehealth.com [140.239.39.130] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA11380 for ; Thu, 4 Jan 2001 13:20:20 -0500 Received: by popserver.chealth.com from localhost (router,SLMail V3.2); Thu, 04 Jan 2001 13:24:59 -0500 Received: by popserver.chealth.com from CHRISW (140.239.39.168::mail daemon; unverified,SLMail V3.2); Thu, 04 Jan 2001 13:24:58 -0500 Message-Id: <4.1.20010104121335.00a16e70@140.239.39.130> X-Sender: eoregan@140.239.39.130 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 04 Jan 2001 13:16:32 -0500 To: chemistry@ccl.net From: "Edel O'Regan" Subject: Structure-Based Drug Design conference Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_17136290==_.ALT" X-SLUIDL: C9E5CE93-E10611D4-86670010-5A9B17A2 --=====================_17136290==_.ALT Content-Type: text/plain; charset="us-ascii" January 4, 2001 Hi, Cambridge Healthtech Institute will host a Structure-Based Drug Design conference in Cambridge, MA in April, 2001. Anyone interested can find out more at the following web site. http://www.xensei.com/conferences/2001/sbd/index.htm Edel Edel O'Regan Ph.D. Conference Producer Cambridge Healthtech Institute FAX: 617-630-1325 Phone: 617-630-1323 email: eoregan@healthtech.com --=====================_17136290==_.ALT Content-Type: text/html; charset="us-ascii" January 4, 2001

Hi,
Cambridge Healthtech Institute will host a Structure-Based Drug Design
conference in Cambridge, MA in April, 2001.

Anyone interested can find out more at the following web site.
http://www.xensei.com/conferences/2001/sbd/index.htm

Edel









Edel O'Regan Ph.D.
Conference Producer
Cambridge Healthtech Institute
FAX: 617-630-1325
Phone: 617-630-1323
email: eoregan@healthtech.com --=====================_17136290==_.ALT-- From chemistry-request@server.ccl.net Thu Jan 4 15:20:14 2001 Received: from narnia3.rutgers.edu (narnia3.rutgers.edu [165.230.180.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA11933 for ; Thu, 4 Jan 2001 15:20:14 -0500 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by narnia3.rutgers.edu (8.8.8/8.8.8) with ESMTP id PAA23581 for ; Thu, 4 Jan 2001 15:20:35 -0500 (EST) Message-ID: <3A54DC81.D580A003@eden.rutgers.edu> Date: Thu, 04 Jan 2001 15:26:42 -0500 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: re:Potential Energy Surfaces Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues: Are there any good books, review articles, or tutorials available on the formation and interpretation of Potential Energy Surfaces? I am finding it difficult to get a real "grasp" on the topic >from much of the literature that I have, and would like a thorough, basic introduction. Thanks for all of your help, and all answers will be promptly summarized. Mary O'Connor Doctoral Candidate Rutgers University New Brunswick, NJ From chemistry-request@server.ccl.net Thu Jan 4 16:25:03 2001 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA12591 for ; Thu, 4 Jan 2001 16:25:03 -0500 Received: from cornell.edu ([132.236.170.133]) by cornell.edu (8.9.3/8.9.3) with ESMTP id QAA10912 for ; Thu, 4 Jan 2001 16:25:02 -0500 (EST) Message-ID: <3A54E9B7.D3A760BA@cornell.edu> Date: Thu, 04 Jan 2001 16:23:03 -0500 From: "J. D. Gans" X-Mailer: Mozilla 4.76 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: PrestoPlot: 2D graphing for Windows Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit PrestoPlot: A freely available 2D plotting tool for Win32 Platforms (Windows NT/95/98/00) inspired by Grace/xmgr. ___________________PrestoPlot has the following features ___________________ Plot types: Scatter plot, Line plot, Bar chart, Linear and log plots, Error bars Analysis: Discrete difference derivatives, Integration, Histograms, Plot statistics Data import: Data import from multi-column ASCII files, Scripting, Command line options Annotation: Graph legends, Axes and graph titles, User defined text Visualization: Multiple plots per graph and multiple graphs per page, Cursor based zoom (for both linear and log plots), Double buffered display to reduce flicker, Custom plot colors, Popup menu for zoom, error bar and plot option control, Floating toolbar for common commands and panning the graph view left, right, up and down Output:Print to any Windows printing device, Copy graphs to the Windows Clipboard ___________________ Source code and executable are freely available ___________________ http://lancelot.bio.cornell.edu/jason/presto.html _______________________________________________________________________________________ Jason Gans Shalloway Lab Department of Molecular Biology & Genetics Cornell University From chemistry-request@server.ccl.net Thu Jan 4 21:39:49 2001 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA13796 for ; Thu, 4 Jan 2001 21:39:49 -0500 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id DAA25568 for ; Fri, 5 Jan 2001 03:39:44 +0100 (MET) Date: Fri, 5 Jan 2001 03:39:44 +0100 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: DQS setup Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I know this is really off-topic, but since I am very desperate by now... I have been trying to install dqs on my cluster. I have setup a master and several workers running dqs_execd and have added the workers via qconf -ah. I have setup a queue via qconf -aq, and can see the queue in the workers via qstat -f. When I submit jobs via qsub to the master, all jobs are executed exclusively on the master and none on the workers, which are all iddling. The workers are seen by qconf -sh. Any help is highly appreciated. Peter