From chemistry-request@ccl.net Wed Oct 1 03:19:52 2003 Received: from postfix3-2.free.fr (postfix3-2.free.fr [213.228.0.169]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h917JLmK022239 for ; Wed, 1 Oct 2003 03:19:21 -0400 Received: from linux (lns-th2-8-82-64-126-20.adsl.proxad.net [82.64.126.20]) by postfix3-2.free.fr (Postfix) with ESMTP id 04A5DCF88; Wed, 1 Oct 2003 09:18:59 +0200 (CEST) Content-Type: text/plain; charset="iso-8859-1" From: Konrad Hinsen Organization: CNRS To: "Mark Thompson" , chemistry:at:ccl.net Subject: Re: CCL:Ewald Sums and Amber 1-4 interactions. Date: Wed, 1 Oct 2003 09:24:17 +0200 User-Agent: KMail/1.4.3 References: <000001c37c82$4be5cd10$0200a8c0@planaria> In-Reply-To: <000001c37c82$4be5cd10$0200a8c0@planaria> MIME-Version: 1.0 Message-Id: <200310010924.17582.hinsen:at:cnrs-orleans.fr> X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_UNCONFIRMED_DSBL,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h917JqmK022249 On Tuesday 16 September 2003 20:42, you wrote: > Amber scales the 1-4 electrostatic terms by a scale factor. It's unclear > to me how this should be accounted for in the Ewald method. These By doing a standard Ewald sum (no scaling whatsoever) and then subtracting what was counted too much, i.e. subtracting a few standard Coulomb terms calculated in minimum-image convention. > interactions are already included in the k-space sum and usually are > corrected for in the real-space exclusion correction. Its not clear to me > how the scaled-1-4 term can be accounted for other than to do the > real-space Ewald treatment of the 1-4 term and then multiply in the Amber > scaling term. If you do that, then you have counted the 1-4 term fully in the k-space term but scaled in the real-space term. This is inconsistent, in particular it will make your energies dependent on the Ewald screening parameter. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen:at:cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@ccl.net Wed Oct 1 06:06:20 2003 Received: from zmail.pt ([213.13.155.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h91A5mmK028218 for ; Wed, 1 Oct 2003 06:05:49 -0400 Received: from WorldClient (authenticated user goncalo.justino:at:zmail.pt) by zmail.pt (MDaemon.PRO.v6.8.4.R) with ESMTP id 6-md50000000012.tmp for ; Wed, 01 Oct 2003 10:52:12 +0100 Received: from [194.117.40.12] via WorldClient with HTTP; Wed, 01 Oct 2003 10:52:12 +0100 Date: Wed, 01 Oct 2003 10:52:12 +0100 From: "=?iso-8859-1?Q?Gon=E7alo?= Deira Justino" To: CHEMISTRY:at:ccl.net Subject: Re: CCL:laptops in computational chemistry? MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Message-ID: X-Mailer: ZMAIL.PT 6.8.4 In-Reply-To: <3F97829D:at:webmail.ksu.edu> References: <3F97829D:at:webmail.ksu.edu> X-Authenticated-Sender: goncalo.justino:at:zmail.pt X-Spam-Processed: zmail.pt, Wed, 01 Oct 2003 10:52:12 +0100 (not processed: spam filter disabled) X-Return-Path: goncalo.justino:at:zmail.pt X-MDaemon-Deliver-To: CHEMISTRY:at:ccl.net Reply-To: goncalo.justino:at:zmail.pt X-Spam-Status: No, hits=1.5 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,RCVD_IN_OSIRUSOFT_COM, REFERENCES,REPLY_WITH_QUOTES,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) well, my experience is at least curious. I've been running several computations involving matrixes ~50000*50000 on a desktop with 2,4Ghz pentium 4 with 512Mb ram and on a laptop with Mobile AMD Athlon XP 1700+ and 256 Mb and they run much faster (like, 2 to 5 times faster) on the laptop... can't really understand why. my guess is that the desktop runs on Windows XP Pro and the laptop on Debian Linux.. maybe that's it for me! ____________________________________ Gongalo Deira Campos Justino "Let your mind be free" -----Original Message----- From: seabra To: CHEMISTRY:at:ccl.net Date: Tue, 30 Sep 2003 11:35:24 -0500 Subject: CCL:laptops in computational chemistry? > Hello, > > Has anyone here had any experience trying to run calculations on a > laptop? How > well do the mobile versions of processors work? Any comment is > appreciated. > > Gustavo Seabra. > > ----------------------------------------------------------------- ----- > Gustavo de Miranda Seabra seabra:at:ksu.edu > Graduate Student > Chemistry Department Kansas State University > ----------------------------------------------------------------- ----- > > > > -= 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, jkl:at:ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- +-+-+- > + From chemistry-request@ccl.net Wed Oct 1 03:50:20 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h917nmmK022935 for ; Wed, 1 Oct 2003 03:49:48 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HM200APZI6JS5:at:mailserver.unimi.it> for CHEMISTRY:at:ccl.net; Wed, 01 Oct 2003 09:30:19 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HM200HPYI6IDP:at:smtp.unimi.it> for CHEMISTRY:at:ccl.net; Wed, 01 Oct 2003 09:30:18 +0200 (MEST) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 8172B182B2; Wed, 01 Oct 2003 09:40:44 +0200 (CEST) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 7596A13B42; Wed, 01 Oct 2003 09:40:44 +0200 (CEST) Date: Wed, 01 Oct 2003 09:40:44 +0200 (CEST) From: Alessandro Contini Subject: Re: CCL:laptops in computational chemistry? In-reply-to: <3F97829D:at:webmail.ksu.edu> To: seabra Cc: CHEMISTRY:at:ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 References: <3F97829D:at:webmail.ksu.edu> X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h917oKmK022943 Hi, I used to run calculation on my laptop until my institute bought me a real workstation. The only concern is about cooling, I used to place a fan pointing on the back of my laptop and I placed some spacers under tha case in order to favor a correct airflow. Reguards Alessandro Contini Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini:at:unimi.it On Tue, 30 Sep 2003, seabra wrote: > Hello, > > Has anyone here had any experience trying to run calculations on a laptop? How > well do the mobile versions of processors work? Any comment is appreciated. > > Gustavo Seabra. > > ---------------------------------------------------------------------- > Gustavo de Miranda Seabra seabra:at:ksu.edu > Graduate Student > Chemistry Department Kansas State University > ---------------------------------------------------------------------- > > > > -= 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, jkl:at:ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Wed Oct 1 03:37:35 2003 Received: from cirse.saclay.cea.fr (cirse.saclay.cea.fr [132.166.192.127]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h917b2mK022562 for ; Wed, 1 Oct 2003 03:37:03 -0400 Received: from argiope.saclay.cea.fr (argiope.saclay.cea.fr [132.166.192.108]) by cirse.saclay.cea.fr (8.12.10/8.12.9/CEAnet-Internet.2.0) with ESMTP id h917b3vk014873 for ; Wed, 1 Oct 2003 09:37:03 +0200 (MEST) Received: from muguet.saclay.cea.fr (unverified) by argiope.saclay.cea.fr (Content Technologies SMTPRS 4.3.10) with ESMTP id for ; Wed, 1 Oct 2003 09:35:55 +0200 Received: from penelope.saclay.cea.fr (penelope.saclay.cea.fr [132.166.189.102]) by muguet.saclay.cea.fr (8.12.10/8.12.9/CEAnet-Internet.2.0) with ESMTP id h917b2Rb029644 for ; Wed, 1 Oct 2003 09:37:02 +0200 (MEST) Received: by penelope.saclay.cea.fr with Internet Mail Service (5.5.2653.19) id ; Wed, 1 Oct 2003 09:42:44 +0200 Message-ID: <3808A7D2DCEAD6118B63009027287265014926:at:azurite.saclay.cea.fr> From: VITORGE Pierre 094605 To: "'chemistry:at:ccl.net'" Subject: errata 2 Gb physical Memory for G98W with Windows2000 Date: Wed, 1 Oct 2003 09:37:02 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I made a typing error in my previous message, one should read %mem, not %chk. The correct question is Is it actually possible to use more than 1 Gb physical memory with Gaussian 98 for Windows? I have just increased the Memory of my computer from 1 to 2 Gb. The computer see the 2Mb memory, however, when I typically used card %mem=1500Mb my Gaussian test job did not run, while it was OK with typically card %mem==750Mb I do not know where the problem comme from: Hardware? Microsoft 2000 SP3? Gaussain 98W? The reference of the new memories is exactly the same as that of the old one, both bought from Dell company in March and September 2003 respectively. Pierre Vitorge CEA DEN Saclay DPC/SECR/LSRM & UMR 8587 (CEA-Universite d'Evry-CNRS) Bat.391 Pe.40a 91191 Gif sur Yvette cedex France tel.(+33) 169-08-32-65, secr.: (+33)169-08-32-50, fax:(+33)169-08-32-42 http://perso.club-internet.fr/vitorgen/pierre From chemistry-request@ccl.net Wed Oct 1 09:42:40 2003 Received: from mail-h12-03.cc.ksu.edu (mail-h12-03.cc.ksu.edu [129.130.12.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h91Dg92g003514 for ; Wed, 1 Oct 2003 09:42:09 -0400 Received: from seabra1 (mC29-248.dialin.k-state.net [129.130.229.248]) by mail-h12-03.cc.ksu.edu (8.12.9/8.12.9) with SMTP id h91Dg7GG007348 for ; Wed, 1 Oct 2003 08:42:08 -0500 (CDT) Message-ID: <002401c38821$bce88840$0100a8c0@seabra1> From: "Gustavo Seabra" To: References: <3F97829D(at)webmail.ksu.edu> Subject: CCL: laptops in computational chemistry (II): Processors Date: Wed, 1 Oct 2003 08:41:35 -0500 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 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Spam-Status: No, hits=-0.5 required=7.0 tests=REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I want to theank everyone who answered my first question If there's any interest, I can summarize the results. Now, the answers I got raised another question: Has anyone noted a significant difference between AMD Athlon and Intel P4 processors? (A laptop running in AMD Athlon goes for about HALF the price of a P4 laptop with similar clock.) If I am to run QM calculations on the laptop, I'd be using Linux. so I'm not worried about the operating system. Gustavo. ---------------------------------------------------------------------------- ---- Gustavo Seabra - Graduate Student E-Mail: seabra(at)ksu.edu Phone:(785) 532-6072 Chemistry Department Kansas State University Manhattan, KS 66506-3701 From chemistry-request@ccl.net Wed Oct 1 11:25:33 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h91FP12g006620 for ; Wed, 1 Oct 2003 11:25:02 -0400 Expiry-Date: Wed, 31 Dec 2003 -1:-1:-1 +0000 Reply-To: training*at*accelrys.com To: chemistry*at*ccl.net Cc: Elizabeth Crookenden Subject: CCL: Accelrys Customer Training Workshops for December MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Jeff Nauss Date: Wed, 1 Oct 2003 08:25:01 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 10/01/2003 08:25:02, Serialize complete at 10/01/2003 08:25:02 Content-Type: multipart/alternative; boundary="=_alternative 0054AC7E88256DB2_=" X-Spam-Status: No, hits=5.1 required=7.0 tests=BASE64_ENC_TEXT,RCVD_IN_OSIRUSOFT_COM,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multipart message in MIME format. --=_alternative 0054AC7E88256DB2_= Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: base64 QWNjZWxyeXMgSW5jLiBhcmUgaG9sZGluZyB0aGUgZm9sbG93aW5nIHRyYWluaW5nIHdvcmtzaG9w cyBhdCBsb2NhdGlvbnMgaW4gDQp0aGUgVVMgYW5kIEV1cm9wZSBkdXJpbmcgRGVjZW1iZXIgMjAw My4gVGhlc2UgZXZlbnRzIGFyZSBkZXNpZ25lZCB0byBoZWxwIA0KeW91IGdldCBtb3JlIHZhbHVl IGZyb20geW91ciBBY2NlbHJ5cyBzb2Z0d2FyZSwgaGVscGluZyB5b3UgdG8gYmV0dGVyIA0KYWNj b21wbGlzaCB5b3VyIHJlc2VhcmNoIGdvYWxzLg0KDQpDb3N0cyBhcmUgJDYwMCBwZXIgZGF5IGZv ciBjb21tZXJjaWFsLCAkNTIwIHBlciBkYXkgZm9yIGdvdmVybm1lbnQgYW5kIA0KJDM4MCBwZXIg ZGF5IGZvciBhY2FkZW1pYyBwbHVzIHRheGVzIGFzIGFwcHJvcHJpYXRlLg0KDQpSYXRpb25hbCBE cnVnIERlc2lnbjoNCkludHJvZHVjdGlvbiB0byBDZXJpdXMyIGZvciBMaWZlIFNjaWVuY2UNCjJu ZC0zcmQgRGVjZW1iZXIgMjAwMywgU2FuIERpZWdvLCBDQQ0KDQpTbWFsbCBNb2xlY3VsZSBhbmQg RHJ1ZyBEZXNpZ24gd2l0aCBDZXJpdXMyDQo0dGgtNXRoIERlY2VtYmVyIDIwMDMsIFNhbiBEaWVn bywgQ0ENCg0KSW50cm9kdWN0aW9uIHRvIENlcml1czIgZm9yIExpZmUgU2NpZW5jZQ0KOXRoLTEw dGggRGVjZW1iZXIgMjAwMywgQnVybGluZ3RvbiwgTUENCg0KU21hbGwgTW9sZWN1bGUgYW5kIERy dWcgRGVzaWduIHdpdGggQ2VyaXVzMg0KMTF0aC0xMnRoIERlY2VtYmVyIDIwMDMsIEJ1cmxpbmd0 b24sIE1BDQoNCg0KQ2hlbWluZm9ybWF0aWNzOg0KDQpBY2NvcmQgRW50ZXJwcmlzZSBDbGllbnQN Cjl0aCBOb3ZlbWJlciAyMDAzLCBTYW4gRGllZ28sIENBDQoNCkRTIEFjY29yZCBmb3IgRXhjZWwg RW50ZXJwcmlzZQ0KMTB0aCBEZWNlbWJlciAyMDAzLCBTYW4gRGllZ28sIENBDQoNCkFjY29yZCBJ bnZlbnRvcnkNCjExdGggRGVjZW1iZXIgMjAwMywgU2FuIERpZWdvLCBDQQ0KDQpBY2NvcmQgSFRT DQoxMnRoIERlY2VtYmVyIDIwMDMsIFNhbiBEaWVnbywgQ0ENCg0KRElWQQ0KMTN0aCBEZWNlbWJl ciAyMDAzLCBTYW4gRGllZ28sIENBDQoNCkFjY29yZCBFbnRlcnByaXNlIEluZm9ybWF0aWNzIERh dGFiYXNlIEFkbWluaXN0cmF0aW9uDQoxNnRoIOKAkyAxN3RoIERlY2VtYmVyIDIwMDMsIFNhbiBE aWVnbywgQ0ENCg0KRm9yIGNvdXJzZSBkZXRhaWxzIGFuZCByZWdpc3RyYXRpb24gc2VlOg0KaHR0 cDovL3d3dy5hY2NlbHJ5cy5jb20vdHJhaW5pbmcvY2hlbWluZi9zY2hlZHVsZS5odG1sIA0KDQoN Ck1hY3JvbW9sZWN1bGFyIE1vZGVsaW5nOg0KDQpJbnRyb2R1Y3Rpb24gdG8gTGlmZSBTY2llbmNl IE1vZGVsaW5nIHdpdGggSW5zaWdodElJDQo5dGgtMTB0aCBEZWNlbWJlciAyMDAzLCBDYW1icmlk Z2UsIFVLDQoNCkhvbW9sb2d5IEJhc2UgUHJvdGVpbiBEZXNpZ24NCjExdGgtMTJ0aCBEZWNlbWJl ciAyMDAzLCBDYW1icmlkZ2UsIFVLDQoNClN0cnVjdHVyZSBCYXNlZCBEcnVnIERlc2lnbiB3aXRo IEluc2lnaHRJSQ0KMTV0aC0xNnRoIERlY2VtYmVyIDIwMDMsIENhbWJyaWRnZSwgVUsNCg0KQ0hB Uk1tDQoxN3RoIOKAkzE4dGggRGVjZW1iZXIgMjAwMywgQ2FtYnJpZGdlLCBVSw0KDQpGb3IgY291 cnNlIGRldGFpbHMgYW5kIHJlZ2lzdHJhdGlvbiBzZWU6IA0KaHR0cDovL3d3dy5hY2NlbHJ5cy5j b20vdHJhaW5pbmcvbWFjcm8vc2NoZWR1bGUuaHRtbCANCg0KRWxpemFiZXRoIENyb29rZW5kZW4N ClRyYWluaW5nIENvLW9yZGluYXRvcg0KDQpBY2NlbHJ5cyBMdGQNCjMzNCBDYW1icmlkZ2UgU2Np ZW5jZSBQYXJrDQpDYW1icmlkZ2UgQ0I0IDBXTiBVSw0KDQpUZWxlcGhvbmUgbnVtYmVyOiArNDQg KDApIDEyMjMgMjI4NjkxDQpGYXggbnVtYmVyOiArNDQgKDApIDEyMjMgMjI4NTAxDQpXZWI6IGh0 dHA6Ly93d3cuYWNjZWxyeXMuY29tDQoNCg0KLS0NCkplZmZyZXkgTC4gTmF1c3MsIFBoLkQuDQpN YW5hZ2VyLCBEaXNjb3ZlcnkgU3R1ZGlvIFRyYWluaW5nDQoNCkFjY2VscnlzIEluYy4NCjk2ODUg U2NyYW50b24gUm9hZA0KU2FuIERpZWdvLCBDQSA5MjEyMS0zNzUyDQoNClBob25lOiA4NTgtNzk5 LTU1NTUNCkZheDogODU4LTc5OS01MTAwDQpFLW1haWw6IGpuYXVzc0BhY2NlbHJ5cy5jb20NCmh0 dHA6Ly93d3cuYWNjZWxyeXMuY29tL3RyYWluaW5nDQoNCg== --=_alternative 0054AC7E88256DB2_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
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E-mail: jnauss*at*accelrys.com
http://www.accelrys.com/training
 --=_alternative 0054AC7E88256DB2_=-- From chemistry-request@ccl.net Wed Oct 1 11:07:46 2003 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 h91F7E2g006330 for ; Wed, 1 Oct 2003 11:07:14 -0400 To: chemistry*at*ccl.net Subject: CC on MacOS X 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, 1 Oct 2003 17:07:10 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.07a |May 14, 2001) at 01/10/2003 17:07:18, Serialize complete at 01/10/2003 17:07:18 Content-Type: multipart/alternative; boundary="=_alternative 00530E0EC1256DB2_=" X-Spam-Status: No, hits=2.3 required=7.0 tests=HTML_10_20,HTML_MESSAGE,NO_REAL_NAME version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multipart message in MIME format. --=_alternative 00530E0EC1256DB2_= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, MOE, Spartan, JChem run on MacOS X. ISIS Base/Draw, ChemOffice and SciLab = are MacOS 9.x applications, thus they also can be used in the new=20 environment. As MacOS X actually is a UNIX os, thus most of the applications created=20 for UNIX can be used here, if one has a C or ForTran compiler and the=20 source code. Some programs have been compiled to MacOS X, see: http://www.apple.com/downloads/macosx/math=5Fscience/index.html. I am a Mac-fan, but I could hardly believe that the price/performance=20 ratio of a linux system (considered available compiled applicatons, as=20 well) could be reached by a Mac. Best regards, Andr=E1s Borosy PhD Computational Chemist Givaudan D=FCbendorf AG Fragrance Research Ueberlandstr. 138 8600 D=FCbendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy*at*givaudan.com --=_alternative 00530E0EC1256DB2_= Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

MOE, Spartan, JChem run on  Mac= OS X. ISIS Base/Draw, ChemOffice and SciLab are MacOS 9.x applications, thu= s they also can be used in the new environment.

As MacOS X actually is a UNIX os, th= us most of the applications created for UNIX can be used here, if one has a= C or ForTran compiler and the source code. Some programs have been compile= d to MacOS X, see:

http://www.apple.com/downloads/macos= x/math=5Fscience/index.html.

I am a Mac-fan, but I could hardly b= elieve that the price/performance ratio of a linux system (considered avail= able compiled applicatons, as well) could be reached by a Mac.

Best regards,

Andr=E1s Borosy
PhD Computational Chemist
Givaudan D=FCbendorf AG
Fragrance Research
Ueberlandstr. 138
8600 D=FCbendorf
Switzerland
tel: + 41-1-8242164
fax: +41-1-8242926
e-mail: andras.borosy*at*givaudan.com --=_alternative 00530E0EC1256DB2_=-- From chemistry-request@ccl.net Wed Oct 1 14:05:11 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h91I4d2g010335 for ; Wed, 1 Oct 2003 14:04:39 -0400 Received: from dopey (dopey.ccmr.cornell.edu [128.84.241.121]) by cornell.edu (8.9.3p2/8.9.3) with SMTP id OAA18288 for ; Wed, 1 Oct 2003 14:04:40 -0400 (EDT) Message-ID: <001501c38846$7be2df60$6400000a[at]ccmr.cornell.edu> From: "Connie Chang" To: Subject: CCL: G03W and electronic structure information Date: Wed, 1 Oct 2003 14:04:39 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0012_01C38824.F47B7E40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=2.1 required=7.0 tests=FROM_ENDS_IN_NUMS,HTML_30_40,HTML_MESSAGE, MAILTO_TO_SPAM_ADDR version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0012_01C38824.F47B7E40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CCLer's, I have a question about the electronic structure information given when = you specify Pop=3DReg in the route section. Why is there a 1PX, 1PY, = etc listed? There's only s-shells at the innermost level. Also, what does it mean to do an optimization in an electric field? = Wouldn't the molecule just tend to be pulled in the direction of the = field? If I optimize first and then do a single point calculation using = Pop=3DReg, would I obtain how the electronic levels are affected by the = imposition of a field? Thank you, Connie Chang cc236[at]cornell.edu ------=_NextPart_000_0012_01C38824.F47B7E40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi CCLer's,
 
I have a question about the electronic = structure=20 information given when you specify Pop=3DReg in the route section.  = Why is=20 there a 1PX, 1PY, etc listed?  There's only s-shells at the = innermost=20 level.
 
Also, what does it mean to do an = optimization in an=20 electric field?  Wouldn't the molecule just tend to be pulled in = the=20 direction of the field?  If I optimize first and then do a single = point=20 calculation using Pop=3DReg, would I obtain how the electronic levels = are affected=20 by the imposition of a field?
 
Thank you,
 
Connie Chang=20 cc236[at]cornell.edu
------=_NextPart_000_0012_01C38824.F47B7E40-- From chemistry-request@ccl.net Wed Oct 1 15:49:08 2003 Received: from p08.es.uci.edu (p08.es.uci.edu [128.200.73.148]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h91Jmb2g011706 for ; Wed, 1 Oct 2003 15:48:37 -0400 Received: from 128.200.204.140 (dhcp-204140.bio.uci.edu [128.200.204.140]) by p08.es.uci.edu (8.11.6/8.11.6) with ESMTP id h91JmV915643 for ; Wed, 1 Oct 2003 12:48:31 -0700 Date: Wed, 1 Oct 2003 12:48:29 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <257947289.20031001124829{at}uci.edu> To: chemistry{at}ccl.net Subject: projection in g03 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCLers, G03 can project normal mode vibrations onto internal coordinates. Who knows about the references of the projection algorithm. Thanks. -- Best regards, Qiang mailto:qiangl{at}uci.edu From chemistry-request@ccl.net Wed Oct 1 16:14:44 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h91KEC2g012231 for >ccl.net>; Wed, 1 Oct 2003 16:14:13 -0400 Received: from cornell.edu (fili.ccmr.cornell.edu [128.84.241.145]) by cornell.edu (8.9.3p2/8.9.3) with ESMTP id QAA00312 for >ccl.net>; Wed, 1 Oct 2003 16:14:11 -0400 (EDT) Message-ID: <3F7B3594.6050509<>cornell.edu> Date: Wed, 01 Oct 2003 16:14:12 -0400 From: Connie Chang >cornell.edu> User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030703 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry<>ccl.net Subject: CCL: Standard Orientation in G03 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.1 required=7.0 tests=FROM_ENDS_IN_NUMS,RCVD_IN_OSIRUSOFT_COM, USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi -- Could someone tell me what is this "standard orientation" that Gaussian puts the molecule in after computations? Is all of the info given by Gaussian -- electronic structure info, vibrational mode info, hessian etc. all given in terms of this standard orientation? Why? Thanks! Connie Chang From chemistry-request@ccl.net Wed Oct 1 16:55:52 2003 Received: from mail.uvigo.es (mail.uvigo.es [193.146.32.91]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h91KtK2g012885 for >ccl.net>; Wed, 1 Oct 2003 16:55:21 -0400 Received: from mail.uvigo.es (localhost [127.0.0.1]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h91KtFYl011067 for >ccl.net>; Wed, 1 Oct 2003 22:55:15 +0200 Received: from correo.uvigo.es (correo.uvigo.es [193.146.32.68]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h91KtF58011062 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for >ccl.net>; Wed, 1 Oct 2003 22:55:15 +0200 Received: from correo (correo [193.146.32.68]) by correo.uvigo.es (8.12.9/8.12.5) with ESMTP id h91KtFXi032588; Wed, 1 Oct 2003 22:55:15 +0200 Date: Wed, 1 Oct 2003 22:55:15 +0200 (CEST) From: Carlos Silva Lopez >uvigo.es> X-X-Sender: To: Connie Chang >cornell.edu> cc: >ccl.net> Subject: Re: CCL:G03W and electronic structure information In-Reply-To: <001501c38846$7be2df60$6400000a<>ccmr.cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h91Ktq2g012900 Hi, 1P functions are commonly used for hydrogen polarization. As long as the electric field affect the electrons behaviour you would have an optimized structure with that perturbation. I do not know if the perturbation is strong enough to affect noticeably the geometry. The population analysis has nothing to do with the electonic levels, it is just an analysis of the density, ususally for the ground state and usually quite arbitrary. You would obtain the effect of the electric field on the ground state of the molecule (or on the state you applied your calculation) Regards _-_-_-_-_-_-_-_-_-_-_-_- Carlos Silva Lspez Dept. Qummica Organica Universidade de Vigo Phone:0034 986812226 -_-_-_-_-_-_-_-_-_-_-_-_ From chemistry-request@ccl.net Wed Oct 1 19:55:36 2003 Received: from adenine.cgl.ucsf.edu (socrates.cgl.ucsf.edu [169.230.27.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h91Nt459004221 for ; Wed, 1 Oct 2003 19:55:05 -0400 Received: from localhost (socrates.cgl.ucsf.edu [169.230.27.3]) by adenine.cgl.ucsf.edu (8.12.10/8.12.9/GSC1.16) with ESMTP id h91Nt4hj974342 for ; Wed, 1 Oct 2003 16:55:04 -0700 (PDT) Date: Wed, 1 Oct 2003 16:55:04 -0700 (PDT) From: Pradipta Bandyopadhyay To: chemistry$at$ccl.net Subject: SHAKE for massless points!! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,USER_AGENT_PINE,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, Does anyone have a code for doing SHAKE or RATTLE for molecules having massless points (like the 4th point in TIP4P)? Any other pointer/paper in this regard will also be appreciated. Pradipta