From chemistry-request@ccl.net Fri Oct 31 02:31:50 2003 Received: from mail.telebit.ru (mail.bancorp.ru [217.107.81.59]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9V7VHLj001879 for ; Fri, 31 Oct 2003 02:31:18 -0500 Received: from 81.25.172.31 ([81.25.172.31] verified) by mail.telebit.ru (CommuniGate Pro SMTP 4.1.6) with ESMTP id 1297391; Fri, 31 Oct 2003 10:31:10 +0300 Date: Fri, 31 Oct 2003 09:49:24 +0300 From: Gregory Shamov X-Mailer: The Bat! (v1.62r) Reply-To: Gregory Shamov Organization: KNC X-Priority: 3 (Normal) Message-ID: <1510089009.20031031094924*at*bancorp.ru> To: Kenneth Geisshirt CC: chemistry*at*ccl.net Subject: CCL:Linux Cluster In-Reply-To: <3FA0CEC5.8010502*at*silex.dk> References: <3FA0CEC5.8010502*at*silex.dk> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,REFERENCES,REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello Kenneth, Thursday, October 30, 2003, 11:41:41 AM, you wrote: KG> A number of companies build clusters (e.g., the one I work for), KG> and you can buy cluster distributions like MandrakeSoft's KG> Clustering product. Finally, you can build a cluster by hand (ok KG> if the number of nodes is less than 6). And what happens if the number of nodes becomes 7 ? Or even 8 ? -- Best regards, Gregory Shamov mailto:gas5x*at*bancorp.ru From chemistry-request@ccl.net Fri Oct 31 09:50:43 2003 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9VEoCLj027099 for ; Fri, 31 Oct 2003 09:50:12 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.12.10/8.12.10) with SMTP id h9VEnZbi025348; Fri, 31 Oct 2003 09:50:11 -0500 (EST) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SAVSMTP 3.1.1.32) with SMTP id M2003103109501123611 ; Fri, 31 Oct 2003 09:50:11 -0500 Received: from sparky.ic.sunysb.edu (sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.12.10/8.12.10) with ESMTP id h9VEoB0h025626; Fri, 31 Oct 2003 09:50:11 -0500 (EST) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id h9VEoB6Y015479; Fri, 31 Oct 2003 09:50:11 -0500 (EST) Date: Fri, 31 Oct 2003 09:50:11 -0500 (EST) From: Yong Liang Yang To: chemistry|at|ccl.net cc: yonyang|at|ic.sunysb.edu Subject: Tips on how to locate TS structures Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) hi, CCL users: I am now trying to locate a TS struture of an epoxide ring open reaction. But I failed many times using QST2 and QST3 method to locate it. I even failed to optimize a "guess" structure which is supposed to be a saddle point on potential energy surface to TS structure. Could anyone give me some tips on how to locate a TS structure effectively? Is there any general procedure to do that? (e.g. do I need a PES scan ? ) Any suggestions would be highly appreciated! Have a good day. Cheers Yong L. Y. From chemistry-request@ccl.net Fri Oct 31 06:32:58 2003 Received: from gw2-mail.cict.fr (gw2-mail.cict.fr [195.220.59.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9VBWQLj016186 for ; Fri, 31 Oct 2003 06:32:26 -0500 Received: from gw2-mail.cict.fr (gw2-mail.cict.fr [127.0.0.1]) by gw2-mail.cict.fr (8.12.10/8.12.9) with ESMTP id h9VBWU01022816 for ; Fri, 31 Oct 2003 12:32:30 +0100 Received: from irsamc.ups-tlse.fr (irsamc.ups-tlse.fr [130.120.88.41]) by gw2-mail.cict.fr (8.12.10/8.12.9) with ESMTP id h9VBWUCT022811 for ; Fri, 31 Oct 2003 12:32:30 +0100 Received: from irsamc4.ups-tlse.fr (irsamc4.ups-tlse.fr [130.120.88.67]) by irsamc.ups-tlse.fr (8.11.6/8.11.6) with ESMTP id h9VBWPs22337 for ; Fri, 31 Oct 2003 12:32:25 +0100 Date: Fri, 31 Oct 2003 12:32:24 +0100 (CET) From: EVANGELISTI Stefano X-X-Sender: stefano|at|irsamc4.ups-tlse.fr To: chemistry|at|ccl.net Subject: CCL: EUCO-CC5 Call for Contributions Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) FIFTH EUROPEAN CONFERENCE ON COMPUTATIONAL CHEMISTRY (EUCO-CC5) GIENS, FRANCE 15-20th June, 2004 >>>>>>>>>>>> CALL for CONTRIBUTIONS <<<<<<<<<<<< The conference is organized by the Working Party on Computational Chemistry of the Federation of European Chemistry Societies (FECS). Local organization will be undertaken by the "Laboratoire de Physique Quantique", of P. Sabatier University, Toulouse (France). Additional information can be found at http://www.irsamc.ups-tlse.fr/EUCOCC5 The conference program will include Plenary Lectures, Oral Communications, and two poster sessions. The following topics will be covered during the conference: Quantum Chemistry Spectroscopy Statistical Mechanics and Thermodynamics Molecular Dynamics and Kinetics Molecular Modelling Cheminformatics and Chemometrics Bioinformatics Oral Communications will be selected on the basis of a written presentation (a manuscript of no more than 6 pages, plus two figures). All these papers will be reviewed, and the selected contributions will be published on the JOURNAL of COMPUTATIONAL METHODS in SCIENCES and ENGINEERING The manuscripts must be sent in electronic form BEFORE december 31, 2003 to eucocc5|at|irsamc.ups-tlse.fr The format must be LaTeX or Word for Windows. Figures must be in .eps or .ps form. We apologize to those who will receive multiple copies of this e-mail. On behalf of the Local Organizing Committee Stefano Evangelisti -- Stefano EVANGELISTI Laboratoire de Physique Quantique Universite Paul Sabatier 118 R.te de Narbonne F-31062 Toulouse FRANCE Phone: +33(0)561.55.76.94 Fax: +33(0)561.55.60.65 E-mail: stefano|at|irsamc.ups-tlse.fr stefano|at|fci.unibo.it From chemistry-request@ccl.net Fri Oct 31 04:40:46 2003 Received: from mail.uct.ac.za (mail.uct.ac.za [137.158.128.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9V9eELj008715 for ; Fri, 31 Oct 2003 04:40:14 -0500 Received: from [137.158.128.125] (helo=anubis.uct.ac.za) by mail.uct.ac.za with esmtp (Exim 3.35 #1) id 1AFVlM-0006k9-00 for chemistry/at/ccl.net; Fri, 31 Oct 2003 11:40:12 +0200 Received: from localhost ([127.0.0.1]) by anubis.uct.ac.za with esmtp (Exim 4.20) id 1AFVln-000EGT-Ok for chemistry/at/ccl.net; Fri, 31 Oct 2003 11:40:39 +0200 Received: from anubis.uct.ac.za ([127.0.0.1]) by localhost (anubis.uct.ac.za [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 54704-03 for ; Fri, 31 Oct 2003 11:40:21 +0200 (SAST) Received: from hydrogen.cem.uct.ac.za ([137.158.164.149] helo=sodium.cem.uct.ac.za) by anubis.uct.ac.za with esmtp (Exim 4.20) id 1AFVlV-000EGE-5M for chemistry/at/ccl.net; Fri, 31 Oct 2003 11:40:21 +0200 Received: from sodium.cem.uct.ac.za (localhost.localdomain [127.0.0.1]) by sodium.cem.uct.ac.za (8.12.8/8.12.8) with ESMTP id h9VNZga2022280 for ; Sat, 1 Nov 2003 01:35:42 +0200 Received: from localhost (csimpson@localhost) by sodium.cem.uct.ac.za (8.12.8/8.12.8/Submit) with ESMTP id h9VNZg8O022276 for ; Sat, 1 Nov 2003 01:35:42 +0200 X-Authentication-Warning: sodium.cem.uct.ac.za: csimpson owned process doing -bs Date: Sat, 1 Nov 2003 01:35:42 +0200 (SAST) From: Chas Simpson X-X-Sender: csimpson/at/sodium.cem.uct.ac.za To: chemistry/at/ccl.net Subject: Re: CCL:Linux (vs FreeBSD) Cluster In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *1AFVlV-000EGE-5M*qy9Um4sF2y6* X-Virus-Scanned: by amavisd-new at anubis.uct.ac.za X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *1AFVln-000EGT-Ok*7aZ/MpaVhto* X-Spam-Status: No, hits=-1.1 required=7.0 tests=IN_REP_TO,SIGNATURE_LONG_DENSE,USER_AGENT_PINE, X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Does anyone have experience building clusters using FreeBSD? If so, are there any benchmarks available in comparison to Linux, preferably with standard chemistry code? What variety of MPI etc. offered the best performance? Thanks, Chas -- _______________________________________________ Chas Simpson Computational Chemistry University of Cape Town South Africa e-mail: csimpson/at/hydrogen.cem.uct.ac.za http://hydrogen.cem.uct.ac.za/compchem/ _______________________________________________ From chemistry-request@ccl.net Fri Oct 31 02:54:36 2003 Received: from collapsed.wormhole.hu (collapsed.wormhole.hu [195.70.35.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9V7s4Lj003039 for ; Fri, 31 Oct 2003 02:54:04 -0500 Received: from szilva (helo=localhost) by collapsed.wormhole.hu with local-esmtp (Exim 3.36 #1 (Debian)) id 1AFU6c-0001YG-00; Fri, 31 Oct 2003 08:54:02 +0100 Date: Fri, 31 Oct 2003 08:54:02 +0100 (CET) From: szilva/at/computer.org X-X-Sender: szilva/at/collapsed.wormhole.hu To: Anil.Nair/at/aventis.com cc: chemistry/at/ccl.net Subject: Re: CCL:Virtual screening In-Reply-To: <7E47908DD24B5243B1FEE5C4E29E7DA70977DC/at/tucsmxsusr01.pharma.aventis.com> Message-ID: References: <7E47908DD24B5243B1FEE5C4E29E7DA70977DC/at/tucsmxsusr01.pharma.aventis.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Szilveszter JUHOS X-Spam-Status: No, hits=-1.7 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,NO_REAL_NAME,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) On Thu, 30 Oct 2003 Anil.Nair/at/aventis.com wrote: > I was wondering whether there is any studies/statistics regarding the success > of virtual screening (including docking and pharmacophore based search) > across different targets and/or target families. Hello, I can speak about docking only, some references: M. Stahl & M. Rarey: Detailed Analysis of Scoring Functions for Virtual Screening J. Med. Chem. 2001, 44, 1035-1042 C. Bissantz, G. Folkers, and D. Rognan: Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations J. Med. Chem. 2000, 43, 4759-4767 Also the Glide tech note is very useful: http://www.schrodinger.com/docs/fd2_2002_2/pdf/fd25_technical_notes.pdf (it is analysing only one docking platform but with many targets, check the "Database enrichment" section). Hope it helps: Szilva From chemistry-request@ccl.net Fri Oct 31 02:59:28 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 h9V7wsLj003282 for ; Fri, 31 Oct 2003 02:58:57 -0500 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 <0HNM00M1P3I5A1$at$mailserver.unimi.it> for chemistry$at$ccl.net; Fri, 31 Oct 2003 08:58:54 +0100 (MET) 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 <0HNM00EEL3I4EP$at$smtp.unimi.it> for chemistry$at$ccl.net; Fri, 31 Oct 2003 08:58:52 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 15EE411455; Fri, 31 Oct 2003 09:10:26 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id DD4F711449 for ; Fri, 31 Oct 2003 09:10:26 +0100 (CET) Date: Fri, 31 Oct 2003 09:10:25 +0100 (CET) From: Alessandro Contini Subject: mp2/cc-pvdz optimization To: chemistry$at$ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 X-Spam-Status: No, hits=0.0 required=7.0 tests=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 h9V7xSLj003304 Hi, I'm trying to perform a mp2/cc-pvdz optimization using g98, but the job is readly interrupted. Following is my .com root section and the output with the error message. I get the same error also when trying to perform a sp job on a b3lyp/6-31G** geometry. Does anybody knows what am I doing wrong? -------------------------------------------- %chk=6_alfa_mp2.chk %mem=512MB %nproc=8 #opt mp2/cc-pvdz scf=(tight,direct) opt 6 alfa mp2/cc-pvdz 0 1 -------------------------------------------- Range of M.O.s used for correlation: 19 322 NBasis= 322 NAE= 64 NBE= 64 NFC= 18 NFV= 0 NROrb= 304 NOA= 46 NOB= 46 NVA= 258 NVB= 258 Disk-based method using ON**2 memory for 46 occupieds at a time. Estimated scratch disk usage= -1 words. Inconsistency from DE2Siz in DoE2D. Error termination via Lnk1e in /mcae/g98/l906.exe. Job cpu time: 0 days 0 hours 5 minutes 15.8 seconds. File lengths (MBytes): RWF= 56 Int= 0 D2E= 0 Chk= 2 Scr= 1 --------------------------------------------- Any suggestion will be greatly appreciated 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 From chemistry-request@ccl.net Fri Oct 31 04:12:30 2003 Received: from pasmtp.tele.dk (pasmtp.tele.dk [193.162.159.95]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9V9BuLj007357 for ; Fri, 31 Oct 2003 04:11:57 -0500 Received: from herodot (unknown [62.242.210.149]) by pasmtp.tele.dk (Postfix) with ESMTP id CE0AC1EC363; Fri, 31 Oct 2003 10:11:43 +0100 (CET) Received: from silex.dk (unknown [62.242.210.146]) by herodot (Postfix) with ESMTP id 3195027D65; Fri, 31 Oct 2003 10:11:43 +0100 (CET) Message-ID: <3FA2258B.1010809$at$silex.dk> Date: Fri, 31 Oct 2003 10:04:11 +0100 From: Kenneth Geisshirt Organization: Silex Science ApS User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5) Gecko/20031024 Debian/1.5-2 StumbleUpon/1.87 X-Accept-Language: da, en MIME-Version: 1.0 To: Gregory Shamov Cc: chemistry$at$ccl.net Subject: Re: CCL:Linux Cluster References: <3FA0CEC5.8010502$at$silex.dk> <1510089009.20031031094924$at$bancorp.ru> In-Reply-To: <1510089009.20031031094924$at$bancorp.ru> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Gregory Shamov wrote: > KG> A number of companies build clusters (e.g., the one I work for), > KG> and you can buy cluster distributions like MandrakeSoft's > KG> Clustering product. Finally, you can build a cluster by hand (ok > KG> if the number of nodes is less than 6). > > And what happens if the number of nodes becomes 7 ? Or even 8 ? My point is that building a cluster by hand does not scale well. If you plan a large cluster (32+ nodes) you will need some kind of automated tool. If you build a 4-node cluster and add a new node (different hardware e.g., an old office pc) you can do it by hand. Kneth -- Kenneth Geisshirt - Principal Scientist Silex Science ApS, Trekronergade 126F, 4. sal, DK-2500 Valby, Denmark Phone: +45 4058 2178 - Fax: +45 3644 3539 - Web: www.silex.dk From chemistry-request@ccl.net Fri Oct 31 02:16:14 2003 Received: from nankai.edu.cn (sun.nankai.edu.cn [202.113.16.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9V7FTLj000956 for ; Fri, 31 Oct 2003 02:15:36 -0500 Received: (eyou send program); Fri, 31 Oct 2003 15:15:48 +0800 Received: from unknown (HELO 192.168.0.100) (unknown@128.195.87.184) by 202.113.16.21 with SMTP; Fri, 31 Oct 2003 15:15:48 +0800 Date: Fri, 31 Oct 2003 00:14:17 -0800 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <14810138681.20031031001417$at$joyie.com> To: chemistry$at$ccl.net Subject: basis sets for water cluster MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.7 required=7.0 tests=FROM_ENDS_IN_NUMS version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi cclers, I need suggestions about water cluster simulation. Do you think B3LYP/6-311++G(d,p) is good enough? I heard that DFT methods have difficulty with weakly-bound complexes. Should I use mp2 other than DFT? Another question is that does two + is necessary here? -- Best regards, John From chemistry-request@ccl.net Fri Oct 31 07:26:52 2003 Received: from kuzey.cc.boun.edu.tr (kuzey.cc.boun.edu.tr [193.140.192.30]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9VCQCLj019425 for ; Fri, 31 Oct 2003 07:26:16 -0500 Received: (qmail 90725 invoked from network); 31 Oct 2003 12:22:09 -0000 Received: from unknown (HELO guardian2.cc.boun.edu.tr) (193.140.192.10) by 0 with SMTP; 31 Oct 2003 12:22:09 -0000 Received: from saritepe.cc.boun.edu.tr ([193.140.192.31]) by guardian2.cc.boun.edu.tr (SAVSMTP 3.1.2.35) with SMTP id M2003103114241204169 for ; Fri, 31 Oct 2003 14:24:12 +0200 Received: (qmail 92144 invoked by uid 80); 31 Oct 2003 15:25:53 -0000 Received: from kimya8.chem.boun.edu.tr (kimya8.chem.boun.edu.tr [193.140.211.238]) by webmail.boun.edu.tr (IMP) with HTTP for ; Fri, 31 Oct 2003 15:25:53 +0000 Message-ID: <1067613953.3fa27f01ebfc8!at!webmail.boun.edu.tr> Date: Fri, 31 Oct 2003 15:25:53 +0000 From: Kevser Gocmen Topal To: srwhttl!at!mta.ca Cc: chemistry!at!ccl.net Subject: CCL:Missing hydrogens: Viewing pdb crystal structures with Spartan and Gaussview03 References: <1067534372.3fa14824f3402!at!webmail.mta.ca> In-Reply-To: <1067534372.3fa14824f3402!at!webmail.mta.ca> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.1 X-Spam-Status: No, hits=-2.3 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi when it asks `to add missing hydrogens` click NO and carry on that is what i am doing best regards Quoting srwhttl!at!mta.ca: > Hi everyone, > > I am having trouble trying to look at a crystal strucutre (from the Protein > data bank). The veiwing programs I have tried (Spartan and Gaussview03) both > > ask me if I want "to add missing hydrogens", when I initally open the file. I > > click yes, but then it appears that the program has missed adding some > hydrogens. This changes the multiplicity and charge, so it differs from the > > pdb file I want. > > Are there any suggestion to aovid this? If not, what are some other programs > > that have both viewing and building/editing capabilites (like spartan and > Gaussiview) where I look at these crystal structures? > > Thanksing you in advance, > Sarah Whittleton > Mount Allison University > Sackville, N.B., Canada > > > -= 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 Fri Oct 31 10:43:53 2003 Received: from ms-smtp-01-eri0.southeast.rr.com (ms-smtp-01-lbl.southeast.rr.com [24.25.9.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9VFhMLj030116 for ; Fri, 31 Oct 2003 10:43:22 -0500 Received: from bobcat (rdu26-84-136.nc.rr.com [66.26.84.136]) by ms-smtp-01-eri0.southeast.rr.com (8.12.10/8.12.7) with ESMTP id h9VFhJQU019476 for ; Fri, 31 Oct 2003 10:43:20 -0500 (EST) Message-ID: <006c01c39fc5$a7e19b60$88541a42@bobcat> From: "Robert Duke" To: Subject: PMEMD 3.1 Release - High Scalability Update to PMEMD Date: Fri, 31 Oct 2003 10:42:56 -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 5.50.4807.1700 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-Virus-Scanned: Symantec AntiVirus Scan Engine 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) We are proud to announce the release of version 3.1 (the first major performance update) of PMEMD (Particle Mesh Ewald Molecular Dynamics). PMEMD is a new version of the Amber module "Sander", and has been written with the major goal of improving performance in Particle Mesh Ewald molecular dynamics simulations and minimizations. The code has been totally rewritten in Fortran 90, and is capable of running in either an Amber 6 or Amber 7 mode. Functionality is more complete in Amber 6 mode, with the Amber 7 mode designed mostly to do the same sorts of things that Amber 6 does, but with output that is comparable to Amber 7 Sander. The calculations done in PMEMD are intended to replicate either Sander 6 or Sander 7 calculations within the limits of roundoff errors. The calculations are just done more rapidly in about half the memory, and runs may be made efficiently on significantly larger numbers of processors. The primary site for high scalability work on PMEMD 3.1 has been the Edinburgh Parallel Computing Centre (IBM P690 Regatta, 1.3 GHz Power4 CPU's, 1280 total processors), and we would like to thank EPCC for making their facilities available for this work. At EPCC, we have obtained maximum throughputs of 3.65 nsec/day (constant volume, 320 processors) and 3.48 nsec/day (constant pressure, 320 processors) for a 90906 atom PME solvated protein simulation. This compares to 0.41 nsec/day (constant pressure, 128 processors) for Sander 7 on the same simulation problem and 3.43 nsec/day (1024 processors) for NAMD on a similar simulation problem (92,224 atoms). More significant is performance at the "50% scalability point", the point where adding more processors will decrease compute efficiency below 50%. PMEMD 3.1 runs the above simulation with at least 50% scalability on 128 processors, producing 2.85 nsec/day throughput. For Sander 7, only 16 processors may be used without going below 50% scalability, and throughput is 0.28 nsec/day. For NAMD, 256 processors may be used at 50% scalability, but throughput is only 1.3 nsec/day. Additional benchmark data is presented in the Update Note available at the Amber website. PMEMD was developed by Dr. Robert Duke in Prof. Lee Pedersen's Lab at UNC-Chapel Hill, starting from the version of Sander in Amber 6. Funding support was provided by NIH grant HL-06350 (PPG) and NSF grant 2001-0759-02 (ITR/AP). When citing PMEMD (Particle Mesh Ewald Molecular Dynamics) in the literature, please use both the Amber Version 7 citation given in the Amber 7 manual, and the following citation: Robert E. Duke and Lee G. Pedersen (2003) PMEMD 3.1, University of North Carolina-Chapel Hill PMEMD is available without charge to users who have an existing license for Amber (version 6 or 7). For more information, and to download the code, please go to: http://amber.scripps.edu/pmemd-get.html - Robert Duke (UNC-Chapel Hill) and David Case (The Scripps Research Institute) From chemistry-request@ccl.net Fri Oct 31 10:52:21 2003 Received: from webmail.universiabrasil.net (smtp.antigosalunos.com.br [200.173.9.134] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9VFpmLj030841 for ; Fri, 31 Oct 2003 10:51:49 -0500 Received: from universiabrasil.net (localhost [127.0.0.1]) by webmail.universiabrasil.net (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HNM00L9ZS31XM(at)webmail.universiabrasil.net> for chemistry(at)ccl.net; Fri, 31 Oct 2003 19:49:49 +0300 (GMT) Received: from [150.161.200.40] by webmail.universiabrasil.net (mshttpd); Fri, 31 Oct 2003 13:49:49 -0300 Date: Fri, 31 Oct 2003 13:49:49 -0300 From: Mozart Subject: Building NWChem 4.5 on windows To: chemistry(at)ccl.net Message-id: MIME-version: 1.0 X-Mailer: iPlanet Webmail Content-type: text/plain; charset=iso-8859-1 Content-language: pt Content-disposition: inline X-Accept-Language: pt X-Spam-Status: No, hits=1.3 required=7.0 tests=RCVD_IN_RFCI,X_ACCEPT_LANG version=2.55 X-Spam-Level: * 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 h9VFqLLj030874 Dear CCL'ers, I've tried to build NWChem 4.5 on Windows and everything was fine, till the link moment, where i've got the following messages: 'C:\nwchem\src>nmake link Microsoft (R) Program Maintenance Utility Version 6.00.8168.0 Copyright (C) Microsoft Corp 1988-1998. All rights reserved.' f90 -nologo /Fe"c:\nwchem\bin\win32 \nw32.exe" .\obj\nwchem.obj .\obj\st ubs_win32.obj /link /stack:20000000 /debug:full /debugtype:cv /pdb:none /libpat h:"c:\nwchem\lib\win32" /libpath:"c:\nwchem\src\tools\lib\win32" /libpa th:"C:\A rquiv~1\MPICH\SDK\lib" nwctask.lib ccsd.lib mcscf.lib selci.lib mp2.lib moints. lib stepper.lib driver.lib dftgrad.lib nwdft.lib gradients.lib cphf.lib esp.lib ddscf.lib guess.lib hessian.lib vib.lib nwcutil.lib rimp2.lib tce.lib tddft.lib property.lib nwints.lib prepar.lib nwmd.lib paw.lib pspw.lib nwpw.lib band.lib n wpwlib.lib cafe.lib space.lib analyze.lib pfft.lib dplot.lib nbo.lib drdy.lib qm mm.lib qmd.lib etrans.lib nwcutil.lib pario.lib global.lib ma.lib peigs.lib t cgmsg-mpi.lib armci.lib lapack.lib blas.lib C:\Arquiv~1 \MPICH\SDK\lib\mpich.lib wsock32.lib imsl.lib imsls_err.lib imslmpistub.lib nwcutil.lib(bas_checksum.obj) : error LNK2001: unresolved external symbol _CHECK SUM_INIT@0 nwcutil.lib(geom_checksum.obj) : error LNK2001: unresolved external symbol _CHEC KSUM_INIT@0 nwcutil.lib(bas_checksum.obj) : error LNK2001: unresolved external symbol _CHECK SUM_UPDATE@8 nwcutil.lib(geom_checksum.obj) : error LNK2001: unresolved external symbol _CHEC KSUM_UPDATE@8 nwcutil.lib(bas_checksum.obj) : error LNK2001: unresolved external symbol _CHECK SUM_CHAR_UPDATE@8 nwcutil.lib(geom_checksum.obj) : error LNK2001: unresolved external symbol _CHEC KSUM_CHAR_UPDATE@8 nwcutil.lib(bas_checksum.obj) : error LNK2001: unresolved external symbol _CHECK SUM_FINAL@8 nwcutil.lib(geom_checksum.obj) : error LNK2001: unresolved external symbol _CHEC KSUM_FINAL@8 paw.lib(paw_sd.obj) : error LNK2001: unresolved external symbol _INIT_PAW_VLOC_M ATRIX@0 paw.lib(paw_sd.obj) : error LNK2001: unresolved external symbol _PAW_COMP_CHARGE _INIT@0 paw.lib(paw_sd.obj) : error LNK2001: unresolved external symbol _PAW_NONLOCAL_IN IT@8 paw.lib(paw_sd.obj) : error LNK2001: unresolved external symbol _PAW_NONLOCAL_EN D@0 paw.lib(paw_sd.obj) : error LNK2001: unresolved external symbol _PAW_COMP_CHARGE _END@0 paw.lib(paw_sd.obj) : error LNK2001: unresolved external symbol _END_PAW_VLOC_MA TRIX@0 paw.lib(paw_force.obj) : error LNK2001: unresolved external symbol _PAW_NONLOC_G OP_U_PTR@4 paw.lib(paw_force.obj) : error LNK2001: unresolved external symbol _PAW_NONLOC_G OP_D_PTR@4 paw.lib(paw_inner_loop.obj) : error LNK2001: unresolved external symbol _PAW_COM P_CHARGE_UPDATE@0 paw.lib(paw_inner_loop.obj) : error LNK2001: unresolved external symbol _PAW_ENE RGY_VLOC_ATOM@0 paw.lib(paw_psi_H.obj) : error LNK2001: unresolved external symbol _PAW_NONLOCAL @24 c:\nwchem\bin\win32\nw32.exe : fatal error LNK1120: 15 unresolved externals NMAKE : fatal error U1077: 'f90' : return code '0x460' Stop.' Can anyone help me in understanding what's happening, and how can i build the program? Thanks a lot. Mozart Pimentel DQF-UFPE-Brazil ------------------------------------------------------------------------ Universia, o portal dos universitarios. Servigos, informagues e contezdo acadjmico na maior rede universitaria do mundo. (www.universiabrasil.net) From chemistry-request@ccl.net Fri Oct 31 11:34:53 2003 Received: from front3.chartermi.net (front3.chartermi.net [24.213.60.109]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9VGYLLj001203 for ; Fri, 31 Oct 2003 11:34:22 -0500 Received: from [24.236.135.230] (HELO mmserver) by front3.chartermi.net (CommuniGate Pro SMTP 4.0.6) with SMTP id 408209059; Fri, 31 Oct 2003 11:34:21 -0500 Message-ID: <000a01c39fcc$d4f1b160$0901a8c0@mmserver> From: "Jim Kress" To: "Gregory Shamov" , "Kenneth Geisshirt" Cc: References: <3FA0CEC5.8010502-.at.-silex.dk> <1510089009.20031031094924-.at.-bancorp.ru> Subject: Re: CCL:Linux Cluster Date: Fri, 31 Oct 2003 11:34:18 -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 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=-1.0 required=7.0 tests=QUOTED_EMAIL_TEXT,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > And what happens if the number of nodes becomes 7 ? Or even 8 ? Or even better, what happens if you want to upgrade from (for example) Red Hat 7.3 to 8 or even (horrors) 9? > From my recent experience (i.e. the refusal of the company (from whom I purchased a cluster) to provide upgrade support from Red Hat 7.3 to 8), one must be very careful in their selection of companies to build a cluster. While they may claim they will provide 'unlimited support for the life of the cluster' (as did the company from whom I purchased my cluster) that 'support' is usually (silently) qualified to be limited to 'systems with experienced and dedicated Linux administrators'. If you don't have one, the definition of 'support' degrades radically, unless, of course, you are willing to spend additional thousands of dollars to send your cluster back to the company for them to upgrade at their site. Note, these requirements were never specified in any quotations, correspondence, or any company literature. Jim ----- Original Message ----- From: "Gregory Shamov" To: "Kenneth Geisshirt" Cc: Sent: Friday, October 31, 2003 1:49 AM Subject: CCL:Linux Cluster > Hello Kenneth, > > Thursday, October 30, 2003, 11:41:41 AM, you wrote: > > KG> A number of companies build clusters (e.g., the one I work for), > KG> and you can buy cluster distributions like MandrakeSoft's > KG> Clustering product. Finally, you can build a cluster by hand (ok > KG> if the number of nodes is less than 6). > > And what happens if the number of nodes becomes 7 ? Or even 8 ? > > -- > Best regards, > Gregory Shamov mailto:gas5x-.at.-bancorp.ru > > > -= 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 Fri Oct 31 15:30:18 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9VKTkLj015969 for ; Fri, 31 Oct 2003 15:29:47 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id h9VKTku5008140 for ; Fri, 31 Oct 2003 14:29:46 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id h9VKTkh23859 for ; Fri, 31 Oct 2003 14:29:46 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Fri, 31 Oct 2003 14:29:46 -0600 (CST) From: Jim Phillips To: chemistry-.at.-ccl.net Subject: Re: CCL:PMEMD 3.1 Release - High Scalability Update to PMEMD In-Reply-To: <006c01c39fc5$a7e19b60$88541a42@bobcat> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.4 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL, Since this message and particularly the PMEMD 3.1 update notes (available at http://amber.scripps.edu/pmemd.3.1.UpdateNote.html) spend considerable time on comparisons to NAMD, I feel that a couple of clarifications are in order regarding NAMD performance and benchmarking. My first point is that not all 90K atom simulations are comparable. The bulk of the computation is in the direct nonbonded interactions, which scale roughly as cutoff^3 * numatoms^2 / volume. The apoa1 NAMD benchmark uses a 12A cutoff, the default specified by the CHARMM force field. I can not find any indication of the cutoff distance of the Factor IX benchmark used by PMEMD, but the Amber 7 manual uses an 8A cutoff by default. This difference alone indicates that *NAMD is doing three times more work* than PMEMD, which is hardly fair. An independent comparison of CHARMM, AMBER, and NAMD running the same Joint Amber-Charmm (JAC) 9A cutoff with PME benchmark is available at http://www.scripps.edu/brooks/Benchmarks/ and demonstrates that NAMD 2.4 serial performance is similar to other programs, with some differences depending on platform. Note that NAMD 2.4 is 18 months old and last month's NAMD 2.5 has been observed by users to be up to 40% faster on some platforms, as well as incorporating the scalability advances reported in our SC2002 paper (http://www.sc-2002.org/paperpdfs/pap.pap277.pdf), which received a Gordon Bell Award. NAMD has historically been tuned for HP Alpha and AMD Athlon, with major improvements in 2.5 for Intel IA64 and IA32. NAMD currently runs twice as fast on Itanium 2 as it does on POWER4. Our local users have never used an IBM SP for production, and while NCSA recently acquired several p690s, these were purchased for large shared memory applications and are not cost effective for NAMD simulations (vs our $30K 48-CPU Athlon clusters). Most recent NAMD scalability tuning has been done on PSC's Lemieux, and very little on any IBM SP. There are also serious performance issues with the interaction between the Charm++ (http://charm.cs.uiuc.edu) communication layer used in NAMD and IBM's MPI implementation in which MPI_Isend fails to send data until the next MPI call after the received node has called MPI_Iprobe and posted an MPI_Recv. Charm++ relies on this idiom to implement message driven execution top of MPI, and it works acceptably on other platforms. We are working to address this issue. In conclusion, NAMD is available free of charge as source code or binaries for a dozen platforms and reads CHARMM and AMBER input file formats, so it is relatively painless to run your own benchmarks to decide if NAMD provides a performance benefit for your simulations. Sincerely, James Phillips, Ph.D. Senior Research Programmer for NAMD Development http://www.ks.uiuc.edu/Research/namd/ On Fri, 31 Oct 2003, Robert Duke wrote: > We are proud to announce the release of version 3.1 (the first major > performance update) of PMEMD (Particle Mesh Ewald Molecular Dynamics). > > PMEMD is a new version of the Amber module "Sander", and has been written > with the major goal of improving performance in Particle Mesh Ewald > molecular dynamics simulations and minimizations. The code has been totally > rewritten in Fortran 90, and is capable of running in either an Amber 6 or > Amber 7 mode. Functionality is more complete in Amber 6 mode, with the > Amber 7 mode designed mostly to do the same sorts of things that Amber 6 > does, but with output that is comparable to Amber 7 Sander. The calculations > done in PMEMD are intended to replicate either Sander 6 or Sander 7 > calculations within the limits of roundoff errors. The calculations are just > done more rapidly in about half the memory, and runs may be made efficiently > on significantly larger numbers of processors. > > The primary site for high scalability work on PMEMD 3.1 has been the > Edinburgh Parallel Computing Centre (IBM P690 Regatta, 1.3 GHz Power4 CPU's, > 1280 total processors), and we would like to thank EPCC for making their > facilities available for this work. At EPCC, we have obtained maximum > throughputs of 3.65 nsec/day (constant volume, 320 processors) and 3.48 > nsec/day (constant pressure, 320 processors) for a 90906 atom PME solvated > protein simulation. This compares to 0.41 nsec/day (constant pressure, 128 > processors) for Sander 7 on the same simulation problem and 3.43 nsec/day > (1024 processors) for NAMD on a similar simulation problem (92,224 atoms). > More significant is performance at the "50% scalability point", the point > where adding more processors will decrease compute efficiency below 50%. > PMEMD 3.1 runs the above simulation with at least 50% scalability on 128 > processors, producing 2.85 nsec/day throughput. For Sander 7, only 16 > processors may be used without going below 50% scalability, and throughput > is 0.28 nsec/day. For NAMD, 256 processors may be used at 50% scalability, > but throughput is only 1.3 nsec/day. Additional benchmark data is > presented in the Update Note available at the Amber website. > > PMEMD was developed by Dr. Robert Duke in Prof. Lee Pedersen's Lab at > UNC-Chapel Hill, starting from the version of Sander in Amber 6. Funding > support was provided by NIH grant HL-06350 (PPG) and NSF grant 2001-0759-02 > (ITR/AP). When citing PMEMD (Particle Mesh Ewald Molecular Dynamics) in the > literature, please use both the Amber Version 7 citation given in the Amber > 7 manual, and the following citation: > > Robert E. Duke and Lee G. Pedersen (2003) PMEMD 3.1, University of North > Carolina-Chapel Hill > > PMEMD is available without charge to users who have an existing license for > Amber (version 6 or 7). For more information, and to download the code, > please go to: > > http://amber.scripps.edu/pmemd-get.html > > > - Robert Duke (UNC-Chapel Hill) and David Case (The Scripps Research > Institute) > > > > > -= 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 Fri Oct 31 11:48:41 2003 Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9VGm9Lj002175 for ; Fri, 31 Oct 2003 11:48:09 -0500 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.12.10/8.12.10) with ESMTP id h9VGm8bk014891 for ; Fri, 31 Oct 2003 11:48:08 -0500 (EST) Message-Id: <200310311648.h9VGm8bk014891-.at.-copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Fri, 31 Oct 2003 11:41:01 -0500 Subject: 2nd-order saddle point CAS and GAMESS-US From: "Olga Dmitrenko" To: chemistry-.at.-ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Score: 0.9 DEAR_SOMEBODY,SPAM_PHRASE_00_01 X-Scanned-By: MIMEDefang 2.37 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) Dear All, I am running CASSCF(8,8) optimization of the second-order saddle point structure using GAMESS-US. I've been able to get to the point when ENERGY in the output does not change anymore (delta E is less 1.0E-7), but the MAXIMUM GRADIENT is still higher than default (0.0001). I've got: MAXIMUM GRADIENT = 0.0002278 RMS GRADIENT = 0.0000868 After this point, all my numerous attempts to get it lower failed. Usually I cut optimization step and take the best geometry (with smallest gradient). Sometimes I increase the number of negative eigenvalues. Here is my optimization control card: $STATPT NNEG=2 METHOD=SCHLEGEL NSTEP=6 DXMAX=0.00001 PURIFY=.true. HESS=READ $END I would highly appreciate learning any other possible optimization tricks that can be used within GAMESS-US. * Olga Dmitrenko * Postdoctoral Fellow * Department of Chemistry and Biochemistry * University of Delaware, Newark * Delaware 19716, USA *Tel: (302) 831-0887 * Email: odmitr^at^udel.edu From chemistry-request@ccl.net Fri Oct 31 15:45:10 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9VKicLj017220 for ; Fri, 31 Oct 2003 15:44:39 -0500 Received: from DAVEG-LIFEBOOK.cachesoftware.com (netscreen.cachesoftware.com [12.17.172.74]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h9VKq8d08849; Fri, 31 Oct 2003 12:52:08 -0800 Message-Id: <5.2.1.1.0.20031031115535.03f94ea0.-at-.mail.cachesoftware.com> X-Sender: daveg.-at-.mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Fri, 31 Oct 2003 12:38:11 -0800 To: Yong Liang Yang From: David Gallagher Subject: CCL:Tips on how to locate TS structures Cc: chemistry.-at-.ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=-1.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Yong, When protonated, some epoxides can ring open with very little activation energy. However, the automated tools in CAChe MOPAC 2002 are usually quite good at finding transition states. If you send me the complete reactant and product structures (sketch or 3D files) we'll try and locate the TS geometry for you. Is it in gas phase or a solvent? Then, if you wish, you could use it as a starting structure for refinement with an alternative method. There is a brief guide to locating TS structures with CAChe MOPAC at http://www.cachesoftware.com/pdfs/CACheGuideTransitionStateModel.pdf Regards, David Gallagher CAChe Group, Fujitsu At 09:50 AM 10/31/2003 -0500, Yong Liang Yang wrote: >hi, CCL users: > >I am now trying to locate a TS struture of an epoxide >ring open reaction. But I failed many times using >QST2 and QST3 method to locate it. I even failed to >optimize a "guess" structure which is supposed to be >a saddle point on potential energy surface to TS structure. >Could anyone give me some tips on how to locate a TS structure >effectively? Is there any general procedure to do that? >(e.g. do I need a PES scan ? ) Any suggestions would be >highly appreciated! Have a good day. > > >Cheers > >Yong L. Y. > > > > >-= 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 Fri Oct 31 13:09:22 2003 Received: from mx4.trentu.ca (mx4.trentu.ca [192.75.12.5]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9VI8oLj007785 for ; Fri, 31 Oct 2003 13:08:50 -0500 Received: (qmail 16069 invoked by uid 510); 31 Oct 2003 18:08:50 -0000 Received: from elewars.-at-.trentu.ca by mx4.trentu.ca by uid 501 with qmail-scanner-1.20rc3 (fsecure: 4.50/2111/. spamassassin: 2.55. Clear:RC:1:. Processed in 0.016913 secs); 31 Oct 2003 18:08:50 -0000 X-Qmail-Scanner-Mail-From: elewars.-at-.trentu.ca via mx4.trentu.ca X-Qmail-Scanner: 1.20rc3 (Clear:RC:1:. Processed in 0.016913 secs) Received: from unknown (HELO trentu.ca) (209.42.101.30) by mx4.trentu.ca with SMTP; 31 Oct 2003 18:08:50 -0000 Message-ID: <3FA2A5EE.3C674D6B.-at-.trentu.ca> Date: Fri, 31 Oct 2003 13:11:58 -0500 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: John Lee , chemistry.-at-.ccl.net Subject: CCL:reply, basis sets for water cluster References: <14810138681.20031031001417.-at-.joyie.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.1 required=7.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Re water clusters and basis sets/method You could look at these: Review: M S Gordon, J H Jensen, Acc Chem Res, 1996, 29, 536 Systematic study of basis sets and correlation levels: A Halkier et al; Theoretical Chemistry Accounts, 1997, 97, 150 Very big basis sets: M Schuetz, JPC, 1997, 107, 4597 M Schuetz, JPCA, 1998, 102, 5997 The issue of Chem Rev: 2002, 102(8) "Modelling the magic water clusters..." M W Jerema eta l, JCC, 1993, 14, 1326 (PM3): JCC, 1993, 14, 1326 A paper by Schuetz on the water pentamer and hexamer appeared in or after 1998, I think, but I don't have the ref. EL === John Lee wrote: > Hi cclers, > > I need suggestions about water cluster simulation. Do you think > B3LYP/6-311++G(d,p) is good enough? I heard that DFT methods have > difficulty with weakly-bound complexes. Should I use mp2 other than > DFT? Another question is that does two + is necessary here? > > -- > Best regards, > John > > -= 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 Fri Oct 31 16:59:57 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 h9VLxPLj024171; Fri, 31 Oct 2003 16:59:26 -0500 In-Reply-To: <3FA2A5EE.3C674D6B)at(trentu.ca> To: elewars Cc: chemistry)at(ccl.net, "Computational Chemistry List" , John Lee Subject: Re: CCL:reply, basis sets for water cluster MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Klaus Stark Date: Fri, 31 Oct 2003 15:59:21 -0600 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 10/31/2003 13:59:25, Serialize complete at 10/31/2003 13:59:25 Content-Type: multipart/alternative; boundary="=_alternative 0078CAB286256DD0_=" X-Spam-Status: No, hits=-0.3 required=7.0 tests=EMAIL_ATTRIBUTION,HTML_20_30,HTML_MESSAGE,IN_REP_TO, MAILTO_TO_SPAM_ADDR,QUOTED_EMAIL_TEXT,REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multipart message in MIME format. --=_alternative 0078CAB286256DD0_= Content-Type: text/plain; charset="US-ASCII" Dear John, there is also C. Lee, H. Chen & G. Fitzgerald, J. Chem. Phys, 102 (1994) 1266 in which the authors used BP86 and BLYP functionals for calculating structural and energetic properties of water clusters of up to 20 monomers. Then they fitted a simple function to their results and extrapolated the stability of larger water clusters with a high accuracy up to the limit of ice at 0 K. Best regards Klaus Dr. Klaus Stark Senior Applications Specialist Accelrys Inc. 1042 Kress Street, Houston, TX 77020 Phone: 713-675-5412 Mobile: 858-395-5243 Fax: 713-675-7791 elewars Sent by: "Computational Chemistry List" 10/31/2003 12:11 PM To John Lee , chemistry)at(ccl.net cc Subject CCL:reply, basis sets for water cluster Re water clusters and basis sets/method You could look at these: Review: M S Gordon, J H Jensen, Acc Chem Res, 1996, 29, 536 Systematic study of basis sets and correlation levels: A Halkier et al; Theoretical Chemistry Accounts, 1997, 97, 150 Very big basis sets: M Schuetz, JPC, 1997, 107, 4597 M Schuetz, JPCA, 1998, 102, 5997 The issue of Chem Rev: 2002, 102(8) "Modelling the magic water clusters..." M W Jerema eta l, JCC, 1993, 14, 1326 (PM3): JCC, 1993, 14, 1326 A paper by Schuetz on the water pentamer and hexamer appeared in or after 1998, I think, but I don't have the ref. EL === John Lee wrote: > Hi cclers, > > I need suggestions about water cluster simulation. Do you think > B3LYP/6-311++G(d,p) is good enough? I heard that DFT methods have > difficulty with weakly-bound complexes. Should I use mp2 other than > DFT? Another question is that does two + is necessary here? > > -- > Best regards, > John > > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > -= 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) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --=_alternative 0078CAB286256DD0_= Content-Type: text/html; charset="US-ASCII"
Dear John,

there is also

C. Lee,  H. Chen & G. Fitzgerald,  J. Chem. Phys, 102 (1994) 1266

in which the authors used BP86 and BLYP functionals for calculating structural and energetic properties of
water clusters of up to 20 monomers. Then they fitted a simple function  to their results and extrapolated the
stability of larger water clusters with a high accuracy up to the limit of ice at 0 K.

Best regards

Klaus


Dr. Klaus Stark
Senior Applications Specialist
Accelrys Inc.
1042 Kress Street, Houston, TX 77020
Phone: 713-675-5412
Mobile: 858-395-5243
Fax: 713-675-7791


elewars <elewars)at(trentu.ca>
Sent by: "Computational Chemistry List" <chemistry-request)at(ccl.net>

10/31/2003 12:11 PM

To
John Lee <g03)at(joyie.com>, chemistry)at(ccl.net
cc
Subject
CCL:reply, basis sets for water cluster





Re water clusters and basis sets/method
You could look at these:

Review: M S Gordon, J H Jensen, Acc Chem Res, 1996, 29, 536

Systematic study of basis sets and correlation levels: A Halkier et al;
Theoretical Chemistry Accounts, 1997, 97, 150

Very big basis sets: M Schuetz, JPC, 1997, 107, 4597

M Schuetz, JPCA, 1998, 102, 5997

The issue of Chem Rev: 2002, 102(8)

"Modelling the magic water clusters..." M W Jerema eta l, JCC, 1993, 14, 1326

(PM3): JCC, 1993, 14, 1326

A paper by Schuetz on the water pentamer and hexamer appeared in or after 1998, I
think, but I don't have the ref.


EL
===

John Lee wrote:

> Hi cclers,
>
> I need suggestions about water cluster simulation. Do you think
> B3LYP/6-311++G(d,p) is good enough? I heard that DFT methods have
> difficulty with weakly-bound complexes. Should I use mp2 other than
> DFT? Another question is that does two + is necessary here?
>
> --
> Best regards,
>  John
>
>
> Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net
> HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs
>



-= 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)
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
--=_alternative 0078CAB286256DD0_=-- From chemistry-request@ccl.net Fri Oct 31 17:43:19 2003 Received: from web21204.mail.yahoo.com (web21204.mail.yahoo.com [216.136.131.77]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9VMglLj026566 for ; Fri, 31 Oct 2003 17:42:48 -0500 Message-ID: <20031031224247.30562.qmail)at(web21204.mail.yahoo.com> Received: from [129.109.59.107] by web21204.mail.yahoo.com via HTTP; Fri, 31 Oct 2003 14:42:47 PST Date: Fri, 31 Oct 2003 14:42:47 -0800 (PST) From: IEJMD Subject: CCL: IECMD 2003 - Extended deadline To: chemistry)at(ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii 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) Internet Electronic Conference of Molecular Design 2003 IECMD 2003, November 23 - December 6 http://www.biochempress.com The deadline for the papers submission for IECMD 2003 was extended to November 20, 2003 IECMD 2003 accepts electronic papers in the following categories: Posters Research notes Communications Full papers Reviews Paper Submission Papers should be submitted as Word files to: oiivanci)at(utmb.edu or to: iejmd)at(yahoo.com After the Conference, all accepted papers will be published in IEJMD - the Internet Electronic Journal of Molecular Design. Important Dates November 20, 2003 - Final Papers due November 23, 2003 - Conference begins December 6, 2003 - Conference ends For detailed Instructions for Authors, see http://www.biochempress.com Instruction for authors and a Word template for preparing the paper are available for download. IECMD 2003 will cover all aspects of computer-assisted molecular design applications in chemistry, biochemistry, biology, chemical and pharmaceutical industry, including: Bioinformatics, cheminformatics, genomics, and computational biology Computer-aided organic synthesis Chemical structure and reactivity investigated with molecular mechanics, quantum chemistry, and molecular dynamics methods Definition, calculation and evaluation of novel structural descriptors Chemical database searching, clustering, similarity and diversity measure Prediction of physico-chemical properties with Quantitative Structure-Property Relationships (QSPR) Quantitative Structure-Activity Relationships (QSAR) models for biological activity, toxicity, mutagenicity, and carcinogenicity Prediction of chromatographic retention parameters and design of stationary phases for chromatography Modeling of bioorganic compounds, such as proteins, enzymes, and nucleic acids New algorithms for modeling chemical and biochemical phenomena, such as global optimization methods, simulated annealing, neural networks, genetic algorithms, ant colony algorithm Design of special materials, catalysts, high energy compounds, polymers, molecular machines ********************************* Dr. Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1157 USA __________________________________ Do you Yahoo!? Exclusive Video Premiere - Britney Spears http://launch.yahoo.com/promos/britneyspears/ From ccl@ccl.net Fri Oct 31 19:33:15 2003 -0500 Return-Path: Reply-To: From: "Mark Thompson" To: chemistry*at*ccl.net Subject: CCL: Missing hydrogens: Viewing pdb crystal structures with Spartan and Gaussview03 Date: Fri, 31 Oct 2003 16:24:43 -0800 Message-ID: <000701c3a00e$8c1b1fc0$271ae70c@planaria> Sarah, ArgusView will do what you want and is free for single-user academic faculty and students. Mark Thompson *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 mark*at*arguslab.com http://www.arguslab.com *************************** > Hi everyone, > > I am having trouble trying to look at a crystal strucutre (from the Protein > data bank). The veiwing programs I have tried (Spartan and Gaussview03) both > > ask me if I want "to add missing hydrogens", when I initally open the file. I > > click yes, but then it appears that the program has missed adding some > hydrogens. This changes the multiplicity and charge, so it differs from the > > pdb file I want. > > Are there any suggestion to aovid this? If not, what are some other programs > > that have both viewing and building/editing capabilites (like spartan and > Gaussiview) where I look at these crystal structures? > > Thanksing you in advance, > Sarah Whittleton > Mount Allison University > Sackville, N.B., Canada > From chemistry-request@ccl.net Fri Oct 31 19:25:18 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 hA10OjLj029875 for ; Fri, 31 Oct 2003 19:24:46 -0500 Received: from mail.uvigo.es (localhost [127.0.0.1]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id hA10Oi6c018433 for ; Sat, 1 Nov 2003 01:24:44 +0100 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 hA10Oimb018428 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Sat, 1 Nov 2003 01:24:44 +0100 Received: from correo (correo [193.146.32.68]) by correo.uvigo.es (8.12.9/8.12.5) with ESMTP id hA10OiSP009755 for ; Sat, 1 Nov 2003 01:24:44 +0100 Date: Sat, 1 Nov 2003 01:24:44 +0100 (CET) From: Carlos Silva Lopez X-X-Sender: To: Subject: Fractional occupation numbers In-Reply-To: <14810138681.20031031001417/at/joyie.com> 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 hA10PILj029885 Hello CCLers I have come across with some papers where people used DFT with fractional occupation numbers to recover non-dynamical correlation. But I was not able to find out how can I submit such a jobs with gaussian, even though in this papers I found the authors claimed to have been using g98. In the gaussian website there is no information. Can somebody help me with this? Thanks a lot! _-_-_-_-_-_-_-_-_-_-_-_- Carlos Silva Lspez Dept. Qummica Organica Universidade de Vigo Phone:0034 986812226 -_-_-_-_-_-_-_-_-_-_-_-_