From chemistry-request@server.ccl.net Mon Sep 23 06:55:10 2002 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8NAt9w13684 for ; Mon, 23 Sep 2002 06:55:09 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=mail) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 17tQrr-0001KI-00; Mon, 23 Sep 2002 12:55:07 +0200 Received: from vejas.vdu.lt ([193.219.38.82] helo=TYREX) by vaidila.vdu.lt with esmtp for chemistry@ccl.net id 17tR01-00050B-00; Mon, 23 Sep 2002 13:03:33 +0200 Date: Mon, 23 Sep 2002 12:55:16 +0200 From: Arturas X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: Arturas X-Priority: 3 (Normal) Message-ID: <212358511.20020923125516@vaidila.vdu.lt> To: chemistry@ccl.net Subject: CCL: structure generators Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello CCL'ers, I've checked CCL old archyves and little was found about chemical structure generators. Could anybody point to similar software (except Molgen) ? Best regards Arturas Z From chemistry-request@server.ccl.net Sat Sep 21 18:33:01 2002 Received: from sd.accelrys.com ([64.165.22.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8LMX0w23159 for ; Sat, 21 Sep 2002 18:33:01 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g8LMf0910232 for chemistry@ccl.net; Sat, 21 Sep 2002 15:41:00 -0700 From: Jeffrey Nauss Received: from sandmail01.sd.accelrys.com (sandmail01.sd.accelrys.com [172.30.160.90]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g8LMexf10218 for ; Sat, 21 Sep 2002 15:41:00 -0700 To: chemistry@ccl.net Subject: Accelrys Customer Workshops in Materials Science MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: Date: Sat, 21 Sep 2002 15:32:41 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 09/21/2002 03:32:44 PM, Serialize complete at 09/21/2002 03:32:44 PM Content-Type: text/plain; charset="us-ascii" Accelrys Inc. have the following Materials Science Workshops/Training Events scheduled for the remainder of the year Registration for all events is at http://www.accelrys.com/training/matsci/schedule.html Further details of the course can be found at http://www.accelrys.com/training/matsci/outlines.html EUROPE Materials Science Modelling in Espoo, Finland on 2nd -4th October Molecular Modelling Applied to Nanotechnology in London, UK on 6th November Workshop in Crystal Structure Determination from Powder Diffraction Data in Cambridge on November 11th Introduction to Materials Studio in Cambridge on November 12th Introduction to Polymer Modelling with Materials Studio on November 13th -14th US Introduction to Materials Studio in San Diego on 22nd October and Burlington on 4th November Introduction to Polymer Modelling with Materials Studio in San Diego on 23-24 October and Burlington 5-6 November. If you have any questions about any of the workshops please contact Elizabeth Crookenden, Training Coordinator on +44 1223 228691 or via e-mail at Training@accelrys.com. -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Sat Sep 21 18:36:27 2002 Received: from sd.accelrys.com ([64.165.22.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8LMaRw23186 for ; Sat, 21 Sep 2002 18:36:27 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g8LMiaT10337 for chemistry@ccl.net; Sat, 21 Sep 2002 15:44:36 -0700 From: Jeffrey Nauss Received: from sandmail01.sd.accelrys.com (sandmail01.sd.accelrys.com [172.30.160.90]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g8LMiaf10328 for ; Sat, 21 Sep 2002 15:44:36 -0700 To: chemistry@ccl.net Subject: Accelrys Customer Training in Cheminformatics MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: Date: Sat, 21 Sep 2002 15:36:20 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 09/21/2002 03:36:22 PM, Serialize complete at 09/21/2002 03:36:22 PM Content-Type: text/plain; charset="us-ascii" Accelrys will be hosting several cheminformatics workshops in the next few months. Further details of the training events can be found at http://www.accelrys.com/training/cheminf/outlines.html Registration in on-line at http://www.accelrys.com/training/cheminf/schedule.html Accord Developer Studio in San Diego on 7-8 October Accord for Oracle in San Diego on 9 October Accord Grid Control in San Diego on 10 October Accord CombiChem Add-on in San Diego on 11 October Searching Accelrys Data Content Databases with Accord Database Explorer in San Diego on 6 November and Burlington on 14th November Accord for Access in San Diego in 7th November and Burlington on 13th November Accord for Excel in San Diego on 8th November and Burlington on 12th November If you have any questions about any of the workshops please contact Elizabeth Crookenden, Training Coordinator, on 011 44 1223 228691 or via e-mail at Training@accelrys.com. -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Sat Sep 21 03:44:51 2002 Received: from kdmail2.netcologne.de ([194.8.194.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8L7iow13778 for ; Sat, 21 Sep 2002 03:44:51 -0400 Received: from cosmologic.de (xdsl-195-14-204-30.netcologne.de [195.14.204.30]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id BNP42066; Sat, 21 Sep 2002 09:44:34 +0200 (CEST) Message-ID: <3D8C235F.84A1AF13@cosmologic.de> Date: Sat, 21 Sep 2002 09:44:31 +0200 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Mark Thompson CC: chemistry@ccl.net, jkl@ccl.net Subject: Re: CCL:FW: Onsager equation References: <000101c260ce$5e7c5050$0300a8c0@attbi.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mark, Andy, be careful! The article of Karelson and Zerner is wrong at that place. I explain this in detail in my article "Calculation of UV/Vis Spectra in Solution" J.Phys.Chem. 1996, 100, 3349 Mike Zerner accepted my criticism in personal discussions and agreed that the way in which the electronic polarization contribution is treated in their papers (and in many papers of other authors as well) was wrong! Andreas Mark Thompson schrieb: > > Andy, > > Here is a good journal article that gives one approach to what you are > looking for: > > Karelson and Zerner, J. Phys. Chem. vol 96, 6949-6957, (1992) > > Mark > > ================================= > Mark Thompson, Ph.D. > Planaria Software > PO Box 55207 > Seattle, WA 98155 > > http://www.arguslab.com > FAX: 206-440-3305 > ================================= > > > > > > -----Original Message----- > > > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > > > Behalf Of Ng Man Fai > > > Sent: Wednesday, September 18, 2002 2:44 AM > > > To: CHEMISTRY@ccl.net > > > Subject: CCL:Onsager equation > > > > > > > > > Hi, may I ask that how to implement the Onsager equation for calculating > > > the solvent effect in the excited state calculations? I have changed the > > > ground state fock matrix by adding the dielectric term, but where to put > > > the index of refraction term? > > > > > > Best regards, > > > Andy > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Sep 23 11:11:36 2002 Received: from antivirus2.its.rochester.edu ([128.151.57.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8NFBZw18898 for ; Mon, 23 Sep 2002 11:11:36 -0400 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.11.6/8.11.6) with ESMTP id g8NFBZs06527 for ; Mon, 23 Sep 2002 11:11:35 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.11.6/8.11.6) with SMTP id g8NFBYH06516 for ; Mon, 23 Sep 2002 11:11:34 -0400 (EDT) Received: from mail.rochester.edu (mail.rochester.edu [128.151.224.17]) by mail.rochester.edu (8.12.4/8.12.1) with SMTP id g8NFBXOk023425 for ; Mon, 23 Sep 2002 11:11:33 -0400 (EDT) Sender: weiz@mail.rochester.edu From: "weiz" Reply-to: weiz@mail.rochester.edu To: chemistry@ccl.net Subject: help about the computing ability of my cluster X-Mailer: WebMAIL to Mail Gateway v3.0m Date: Mon, 23 Sep 2002 11:11:33 -0400 Priority: normal Message-id: <3d8f2f25.5b80.12786@mail.rochester.edu> Hi, all: I have a 16 nodes AMD cluster. each node has 2GH CPU. if one project need to be run for 1 hour by 4 processors of a silicon graphic origin 2000. how long it will take if using my cluster. just give me a very rough estimation will be ok!!! thank you very much. wei zhuang weiz@mail.rochester.edu From chemistry-request@server.ccl.net Wed Sep 18 12:57:59 2002 Received: from chemcomp.com ([209.226.194.164]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8IGvtw23568 for ; Wed, 18 Sep 2002 12:57:59 -0400 Received: from chemcomp.ca (smtp.chemcomp.com [209.226.194.167]) by chemcomp.com (8.9.3/8.9.3) with ESMTP id MAA07967 for ; Wed, 18 Sep 2002 12:57:55 -0400 Received: from chemcomp.com (AC932AE2.ipt.aol.com [172.147.42.226]) (authenticated) by chemcomp.ca (8.11.6/8.11.6) with ESMTP id g8IFsZK01938 for ; Wed, 18 Sep 2002 11:54:35 -0400 Message-ID: <3D88B17F.60F49F55@chemcomp.com> Date: Wed, 18 Sep 2002 13:01:51 -0400 From: Pamela Newton Organization: CCG X-Mailer: Mozilla 4.77 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: "CHEMISTRY@ccl.net" Subject: Applications being accepted for CCG Excellence Award Content-Type: multipart/mixed; boundary="------------5DCFC19B69BA23D457C4EB8A" This is a multi-part message in MIME format. --------------5DCFC19B69BA23D457C4EB8A Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Chemical Computing Group (CCG) Excellence Award The Chemical Computing Group (CCG) Excellence Awards were created to stimulate graduate student participation in COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are graduate students in good standing who present work within the COMP program, either in oral or poster format. Winners receive up to $1,150 in travel funding to attend the ACS National meeting, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license for their academic research group. This year, the number of awards per national meeting has been increased to ten, representing $200,000 in support from Chemical Computing Group over a three-year period. Applications for CCG Excellence Awards Awardees are chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students are encouraged to submit applications for the Awards. Awards will be given only to those individuals making presentations, and not to co-authors. To apply, an application must be submitted to the Treasurer of the COMP division for consideration. This application consists of an extended (2-page) abstract of the poster or presentation along with a letter of support from the research advisor, a two page CV, and a personal statement. Secondly, an abstract must be submitted through the ACS OASYS system for online submissions prior to the deadline for the meeting at which the awards will be presented. Send all application materials to: Prof. Curt M. Breneman; Treasurer, ACS COMP Division; Rensselaer Polytechnic University, Department of Chemistry; 110 8th St.; Troy, NY 12180 Deadlines for the ACS National Meeting in New Orleans - March 23-27, 2003: Oct. 15, 2002 - CCG Excellence Award applications due to COMP Treasurer Nov. 1, 2002 - Awardees determined Nov. 15, 2002 - Abstracts submitted via OASYS (http://oasys.acs.org/oasys.htm) for all COMP abstracts, including CCG Awardees Press releases regarding past CCG Awardees and planned COMP symposia for the ACS National Meeting are also available on the ACS COMP division website (http://membership.acs.org/C/COMP/). ________________________ Pamela Newton Director, Sales & Marketing Chemical Computing Group T: 1.514.393.1055 x 28 Cell: 1.514.945.9230 F: 1.514.874.9538 --------------5DCFC19B69BA23D457C4EB8A Content-Type: text/x-vcard; charset=us-ascii; name="pnewton.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Pamela Newton Content-Disposition: attachment; filename="pnewton.vcf" begin:vcard n:Newton;Pamela tel;cell:(514) 945-9230 tel;fax:(514) 874-9538 tel;work:(514) 393-1055 x 28 x-mozilla-html:FALSE url:http://www.chemcomp.com org:Chemical Computing Group, Inc.;Sales/Marketing version:2.1 email;internet:pnewton@chemcomp.com title:Account Manager adr;quoted-printable:;;1010 Sherbrooke St. West=0D=0ASuite 910;Montreal;Quebec;H3A 2R7;Canada fn:Pam Newton end:vcard --------------5DCFC19B69BA23D457C4EB8A-- From chemistry-request@server.ccl.net Mon Sep 23 15:56:32 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8NJuWw24544 for ; Mon, 23 Sep 2002 15:56:32 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id PAA97582; Mon, 23 Sep 2002 15:44:26 -0400 (EDT) Date: Mon, 23 Sep 2002 15:44:26 -0400 From: Rick Venable To: weiz cc: chemistry@ccl.net Subject: Re: CCL:help about the computing ability of my cluster In-Reply-To: <3d8f2f25.5b80.12786@mail.rochester.edu> Message-ID: ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 23 Sep 2002, weiz wrote: > I have a 16 nodes AMD cluster. each node has 2GH CPU. if one > project need to be run for 1 hour by 4 processors of a > silicon graphic origin 2000. how long it will take if using > my cluster. just give me a very rough estimation will be > ok!!! thank you very much. My best guess is under 2 hours for 2 procs on the same node; predictions for more processors aren't so easy. Parallel scaling is application and architecture dependent; while the AMD machines may compare favorably for 1 or 2 proc calculations, that may not be the case for 4, 8, or 16 proc calcs. A key issue is the amount of inter-process communication needed by the application; data intensive MD codes like AMBER and CHARMM don't scale very well on Linux clusters without taking some additional steps. Some examples are: + Use Linux 2.2.x kernel and apply the 'tcpfix' patch + Use Myrinet switch and host PCI boards; expensive I've heard (but haven't tested) that newer machines with the 2.4.x Linux kernel and Gigabit NICs now show a significant improvement in parallel scaling over the use of 100baseT for the ethernet TCP/IP connectivity. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Mon Sep 23 16:26:02 2002 Received: from h123n2fls33o850.telia.com ([217.208.157.123]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8NKQ2w25012 for ; Mon, 23 Sep 2002 16:26:02 -0400 Received: (from spoel@localhost) by h123n2fls33o850.telia.com (8.11.6/8.11.6) id g8NKSiU01676; Mon, 23 Sep 2002 22:28:44 +0200 X-Authentication-Warning: h123n2fls33o850.telia.com: spoel set sender to spoel@xray.bmc.uu.se using -f Subject: Re: CCL:help about the computing ability of my cluster From: David Cc: chemistry@ccl.net In-Reply-To: References: Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.3 (1.0.3-6) Date: 23 Sep 2002 22:28:44 +0200 Message-Id: <1032812924.1634.3.camel@h123n2fls33o850.telia.com> Mime-Version: 1.0 On Mon, 2002-09-23 at 21:44, Rick Venable wrote: > On Mon, 23 Sep 2002, weiz wrote: > > I have a 16 nodes AMD cluster. each node has 2GH CPU. if one > > project need to be run for 1 hour by 4 processors of a > > silicon graphic origin 2000. how long it will take if using > > my cluster. just give me a very rough estimation will be > > ok!!! thank you very much. > > My best guess is under 2 hours for 2 procs on the same node; predictions > for more processors aren't so easy. Assuming perfect scaling on the SGI that would mean 4 hours on a single CPU. The 2 GHz AMD will be 4 to 10 times faster than the SGI, depending on your code, compiler etc., so let us say, between 0.5 and 1 hour on a single AMD chip. Scaling on duals is quite good usually, so: between 0.25 and 0.5 hour on a dual box. Beyond that I agree with Rick, it depends on your network and your problem. Try it out and report back to the list, just for fun. -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Mon Sep 23 22:06:44 2002 Received: from front1.chartermi.net ([24.213.60.123]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8O26hw08968 for ; Mon, 23 Sep 2002 22:06:44 -0400 Received: from [24.247.80.10] (HELO ws610) by front1.chartermi.net (CommuniGate Pro SMTP 3.5.3) with SMTP id 50117184 for chemistry@ccl.net; Mon, 23 Sep 2002 22:06:44 -0400 Message-ID: <001301c2636f$0760f6b0$0401a8c0@kressworks.com> Reply-To: From: To: "CCL" Subject: Printing QEq charges in G98W Date: Mon, 23 Sep 2002 22:06:40 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Will someone please explain to me how to print QEq charges in G98W? I will summarize to the list. Thanks. Jim