From chemistry-request@ccl.net Tue Jan 25 04:17:22 2005 Received: from mailhub1.uq.edu.au (mailhub1.uq.edu.au [130.102.148.128]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0P9HIiL022820 for ; Tue, 25 Jan 2005 04:17:19 -0500 Received: from smtp2.uq.edu.au (smtp2.uq.edu.au [130.102.5.53]) by mailhub1.uq.edu.au (8.12.11/8.12.11) with ESMTP id j0P7ig5e068483; Tue, 25 Jan 2005 17:44:42 +1000 (EST) Received: from uq.edu.au (gonzo.soe.uq.edu.au [130.102.5.131]) by smtp2.uq.edu.au (8.12.10/8.12.10) with ESMTP id j0P7igDQ003129; Tue, 25 Jan 2005 17:44:42 +1000 (EST) Received: from [152.98.207.35] by msg2b.soe.uq.edu.au (mshttpd); Tue, 25 Jan 2005 17:44:42 +1000 From: Dr Seth OLSEN To: "C. Garoufalis" Cc: chemistry..at..ccl.net Message-ID: <89c8088ed5.88ed589c80..at..uq.edu.au> Date: Tue, 25 Jan 2005 17:44:42 +1000 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) MIME-Version: 1.0 Content-Language: en Subject: Re: CCL:parallel GAMESS problems X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.43 on UQ Mailhub X-Spam-Status: No, hits=4.5 required=7.5 tests=IMPRONONCABLE_1,TRACKER_ID autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Christos, I noticed this when I first tested parallel GAMESS on machines here. Increasing the 'shmmax' parameter for the system seemed to help the problem. Linux systems usually have this value set too low to be useful. A value of 256mb seemed for work best for me. Instructions on how to change the parameter can be found in the GAMESS installation documentation. Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Computational Systems Biology Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1..at..uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms ----- Original Message ----- From: "C. Garoufalis" Date: Tuesday, January 25, 2005 2:34 am Subject: CCL:parallel GAMESS problems > Dear CCLers > I have successfully compiled the latest version of GAMESS > on my linux cluster. When running on a single node, everything goes > fine.When I try to run a parallel job there seems to be a problem. > The job starts successfully, but the cpu utilization on the nodes > is less than 1% > As a result the parallel job is much slower than the one run on a > single node. > Obviously, I am missing something > > Dr. Christos S. Garoufalis > Dept. of Physics, Univ. of Patras Greece From chemistry-request@ccl.net Tue Jan 25 04:36:40 2005 Received: from mailhub2.uq.edu.au (mailhub2.uq.edu.au [130.102.149.128]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0P9aaiL023497 for ; Tue, 25 Jan 2005 04:36:37 -0500 Received: from smtp2.uq.edu.au (smtp2.uq.edu.au [130.102.5.53]) by mailhub2.uq.edu.au (8.12.11/8.12.11) with ESMTP id j0P7Yext004694 for ; Tue, 25 Jan 2005 17:34:40 +1000 (EST) Received: from uq.edu.au (gonzo.soe.uq.edu.au [130.102.5.131]) by smtp2.uq.edu.au (8.12.10/8.12.10) with ESMTP id j0P7YeDQ000782 for ; Tue, 25 Jan 2005 17:34:40 +1000 (EST) Received: from [152.98.207.35] by msg2b.soe.uq.edu.au (mshttpd); Tue, 25 Jan 2005 17:34:40 +1000 From: Dr Seth OLSEN To: chemistry..at..ccl.net Message-ID: <8af5a861a1.861a18af5a..at..uq.edu.au> Date: Tue, 25 Jan 2005 17:34:40 +1000 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) MIME-Version: 1.0 Content-Language: en Subject: CCL: PEACH documentation in English? X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.43 on UQ Mailhub X-Spam-Status: No, hits=4.5 required=7.5 tests=IMPRONONCABLE_1,TRACKER_ID autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Colleagues, I am interested in using the PEACH program to carry out Fragment Molecular Orbital calculations and to produce GAMESS input for similar calculations. However, the only documentation I can find for PEACH is in japanese. Does an english version exist? Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Computational Systems Biology Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1..at..uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms From chemistry-request@ccl.net Tue Jan 25 15:49:47 2005 Received: from rojo2.usc.es (rojo2.usc.es [193.144.75.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0PKnkiL015533 for ; Tue, 25 Jan 2005 15:49:46 -0500 Received: from localhost (rojo2 [127.0.0.1]) by rojo2.usc.es (Postfix) with ESMTP id A9AA6D58B4 for ; Tue, 25 Jan 2005 19:46:18 +0100 (CET) Received: from rojo2.usc.es ([127.0.0.1]) by localhost (rojo2 [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 02782-14 for ; Tue, 25 Jan 2005 19:46:18 +0100 (CET) Received: from rojo4.usc.es (rojo4.usc.es [193.144.75.15]) by rojo2.usc.es (Postfix) with ESMTP id 54573D5890 for ; Tue, 25 Jan 2005 19:46:18 +0100 (CET) Received: by rojo4.usc.es (Postfix, from userid 33) id 18973EB5; Tue, 25 Jan 2005 19:46:18 +0100 (CET) Received: from qfatlas.usc.es (qfatlas.usc.es [193.144.74.160]) by correoweb.usc.es (IMP) with HTTP for ; Tue, 25 Jan 2005 19:46:18 +0100 Message-ID: <1106678778.41f693fa11059!at!correoweb.usc.es> Date: Tue, 25 Jan 2005 19:46:18 +0100 From: qftjesus!at!usc.es To: chemistry!at!ccl.net Subject: adding dynamical correlation to CASSCF MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.6 X-Virus-Scanned: amavisd-new at usc.es X-Spam-Status: No, hits=4.0 required=7.5 tests=NO_RDNS2,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear netters: Which are the most appropriate methods to add the dynamical correlation to CASSCF optimized geometries? CASPT2 is used frequently, but Gaussian and Gamess do not include it. Gaussian uses CASSCF-MP2. Is this method reliable? Gamess uses other methods as the multiconfigurational quasi-degenerate secondorder perturbation theory (MCQDPT2) and the CASSCF second-order configuration interaction (CASSCF-SOCI) theory. What about these two methods? I ask for advices. Tnanks Jesus Rodriguez-Otero From chemistry-request@ccl.net Tue Jan 25 19:17:24 2005 Received: from mail.monmouth.edu (mail.monmouth.edu [192.100.64.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0Q0HNiL021605 for ; Tue, 25 Jan 2005 19:17:23 -0500 Received: from monmouth.edu (MU14162.backbone.monmouth.edu [10.1.1.63]) by mail.monmouth.edu (8.12.11/8.12.11) with ESMTP id j0PMpLDI021732; Tue, 25 Jan 2005 17:51:21 -0500 Message-ID: <41F6CD68.8090004=at=monmouth.edu> Date: Tue, 25 Jan 2005 17:51:20 -0500 From: Robert Topper Organization: Chemistry, Med Tech and Physics, Monmouth University User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry=at=ccl.net CC: rtopper=at=monmouth.edu Subject: ECCC10: Awards and Deadline Extension Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.43 X-Spam-Status: No, hits=1.1 required=7.5 tests=FVGT_m_MULTI_ODD2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear colleagues, I hope that you will participate in the upcoming 10th Electronic Computational Chemistry Conference at http://eccc.monmouth.edu. We have extended the deadline for contributions to Tuesday, February 1 in order to encourage the greatest possible participation. We are pleased to announce that for the first time, ECCC10 will feature an award program. The award program is primarily intended for scientists in the early stages of their careers, including graduate and undergraduate students, postdoctoral fellows, and investigators who are in the first few years of a long-term appointment. We also want to especially encourage contributions > from scientists who are working in developing countries. There will be at least two awards given in recognition of the most Outstanding Scientific Presentation. In addition, one award will be given to the authors of the Best Multimedia Presentation. This presentation will be the one which best reflects the online nature of the ECCC conference and makes the most effective use of multimedia to enhance the presentation of the scientific content. The recipients of these awards will be decided by the Scientific Organizing Committee. Two well-known software companies, Parallel Quantum Solutions (http://www.pqs-chem.com) and Schrodinger (http://www.schrodinger.com) have generously provided prizes to the ECCC10 Award winners. PQS plans to provide their PQS quantum chemistry software and a perpetual license on the same hardware. Schrodinger plans to provide a one-year license for a selection of three computing modules plus the Maestro GUI (please note that some contributors may possibly not be eligible for software prizes if there are governmental restrictions beyond our control). We are extremely grateful to PQS and Schrodinger for their generous sponsorship of the ECCC and their support to the international computational chemistry community. For the SOC, Robert Topper -- Robert Q. Topper Chair and Associate Professor Department of Chemistry, Medical Technology and Physics Monmouth University 400 Cedar Avenue West Long Branch, NJ 07764-1898 (732)571-4418 (voice);(732)263-5213 (fax) rtopper=at=monmouth.edu Check out ECCC10 in April 2005! Registration is free! http://eccc.monmouth.edu -- Robert Q. Topper Chair and Associate Professor Department of Chemistry, Medical Technology and Physics Monmouth University 400 Cedar Avenue West Long Branch, NJ 07764-1898 (732)571-4418 (voice);(732)263-5213 (fax) rtopper=at=monmouth.edu Check out ECCC10 in April 2005! Registration is free! http://eccc.monmouth.edu From chemistry-request@ccl.net Tue Jan 25 15:37:01 2005 Received: from mfwj036.mfw.is.co.za (mfwj036.mfw.is.co.za [196.35.77.46]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0PKauiL015114 for ; Tue, 25 Jan 2005 15:36:57 -0500 Received: from zacdbhd02.ag.ad.local (Not Verified[168.210.132.250]) by mfwj036.mfw.is.co.za with NetIQ MailMarshal (v5.5.6.7) id ; Tue, 25 Jan 2005 20:46:40 +0200 Received: from zavrexc01.ag.ad.local ([172.18.20.4]) by zacdbhd02.ag.ad.local with Microsoft SMTPSVC(5.0.2195.6713); Tue, 25 Jan 2005 20:41:04 +0200 X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5030D.6CCA0326" Subject: Re:Orbitals and Reality Date: Tue, 25 Jan 2005 20:41:04 +0200 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Re:Orbitals and Reality Thread-Index: AcUDDWzHGWyJ3dnXS+ecPY2Kc6rMiA== From: "Phala, Noko \(VR\)" To: X-OriginalArrivalTime: 25 Jan 2005 18:41:04.0812 (UTC) FILETIME=[6D0046C0:01C5030D] X-Spam-Status: No, hits=3.0 required=7.5 tests=HTML_MESSAGE,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C5030D.6CCA0326 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Regarding the on-going discussion on 'observation' of orbitals, cant one = of us who think that what was observed was electron density perhaps calcu= late the difference in total density between an N2 and an N2+ molecule to= =20show that the resultant 'net' density is similar to what was observed?= =20Unless they can show us images of 'virtual' orbitals, I will never be= =20convinced that orbitals have suddenly gained physical meaning. Noko Phala AngloGold Ashanti Confidentiality Warning ________________________ This e-mail message contains confidential information which is intended=20 for the use of the person to whom it is addressed. If you received it=20 in error, please notify the sender and delete the material from any=20 computer. Any disclosure, re-transmission, dissemination or any other=20 use of this information is strictly prohibited. ------_=_NextPart_001_01C5030D.6CCA0326 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable The trajectory and the starting structure contain the same number of atoms; I checked to make sure. I also tried including a prmtop file, but that had no effect. Does anyone have any suggestions as to how I might remedy this? If I've left out any crucial information, please let me know. Thanks, Robyn Ayscue kajsicat*at*yahoo.com __________________________________ Do you Yahoo!? Take Yahoo! Mail with you! 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