From chemistry-request@ccl.net Mon Oct 6 05:03:57 2003 Received: from dahlia.noc.ucla.edu (dahlia.noc.ucla.edu [169.232.46.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9693P59005161 for ; Mon, 6 Oct 2003 05:03:25 -0400 Received: from azalea.noc.ucla.edu (azalea.noc.ucla.edu [169.232.47.12]) by dahlia.noc.ucla.edu (8.12.8p2/8.12.8) with ESMTP id h9693JbL006362 for ; Mon, 6 Oct 2003 02:03:19 -0700 Received: from dsievers (23.226.nwc.net [207.151.226.23]) (authenticated bits=0) by azalea.noc.ucla.edu (8.12.9p1/8.12.9) with ESMTP id h9692egG001943 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Mon, 6 Oct 2003 02:03:10 -0700 Message-ID: <000701c38be7$4e6a4740$7700a8c0)at(ucla.triangle.org> From: "Doug Sievers" To: "CCL" Subject: UFF in molecular dynamics Date: Mon, 6 Oct 2003 01:52:46 -0700 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-Probable-Spam: no X-Spam-Hits: 0 X-Scanned-By: vscan.smtp.ucla.edu 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) CCLers, Does anyone know of a molecular dynamics code that can use the Universal Force Field (UFF)? Any free code that is reliable would be favored. If there are any other implementations that might be suitable for modeling organometallic compounds I would be happy to hear about them. Thank you, Douglas Sievers Graduate Student Researcher Materials Science & Engineering 3049 Engineering 1 (310) 794-6491 dsievers)at(ucla.edu From chemistry-request@ccl.net Mon Oct 6 11:15:08 2003 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h96FEb59021514 for >ccl.net>; Mon, 6 Oct 2003 11:14:37 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id CC15E130BBD4; Mon, 6 Oct 2003 17:14:38 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 0135D130BBC8 for >ccl.net>; Mon, 6 Oct 2003 17:14:36 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 6 Oct 03 17:14:32 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 6 Oct 03 17:14:24 +0100 From: "Jens Spanget-Larsen" >virgil.ruc.dk> Organization: Roskilde Universitetscenter To: chemistry<>ccl.net Date: Mon, 6 Oct 2003 17:14:22 +0200 Subject: Excited state polarizabilities Reply-To: spanget<>ruc.dk Message-ID: <3F81A2FC.8019.111FA2F0@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL, I am attempting to compute excited electronic state polarizabilities with Gaussian98 or Gaussian03 by using the keywords CIS and POLAR. I wish to avoid POLAR=EnOnly which is very time consuming. But if I understand the manual correctly, POLAR alone should compute polarizabilities (but not hyperpolarizabilities) for the CIS procedure. However, I cannot make it work. Any help? Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget<>ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Mon Oct 6 02:55:38 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h966t559032486 for ; Mon, 6 Oct 2003 02:55:06 -0400 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1A6PGq-000NGMC; Mon, 6 Oct 2003 08:55 +0200 Message-ID: <3F7C499E.7040608.-at-.chem.vu.nl> Date: Thu, 02 Oct 2003 17:51:58 +0200 From: Anton Feenstra User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.3.1) Gecko/20030425 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Pradipta Bandyopadhyay CC: chemistry.-at-.ccl.net Subject: CCL:SHAKE for massless points!! References: In-Reply-To: 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) Pradipta Bandyopadhyay wrote: > 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. It is implemented in Gromacs, but I don't have a reference ready. I also don't know in which Gromacs version this first appeared. Also in Gromacs we have massless interaction points (called 'dummy atoms' in the manual) whose position is generated from linear combinations of positions of other atoms, and forces are back- distributed accordingly. Check www.gromacs.org for online manual. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra.-at-.chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Mon Oct 6 13:21:27 2003 Received: from llar.net.uniovi.es (llar.net.uniovi.es [156.35.11.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h96HKt59027703 for ; Mon, 6 Oct 2003 13:20:55 -0400 Received: from CONVERSION-DAEMON.llar.net.uniovi.es by llar.net.uniovi.es (PMDF V6.1 #39514) id <01L1IPTIA7OG01244F..at..llar.net.uniovi.es> for chemistry..at..ccl.net; Mon, 06 Oct 2003 19:20:35 +0200 (MET) Received: from webuniovi.innova.uniovi.es (webuniovi.innova.uniovi.es [156.35.33.99]) by llar.net.uniovi.es (PMDF V6.1 #39514) with ESMTP id <01L1IPTENLYK011V2R..at..llar.net.uniovi.es> for chemistry..at..ccl.net; Mon, 06 Oct 2003 19:20:29 +0200 (MET) Received: from localhost ([127.0.0.1] helo=pcc134.quimica.uniovi.es ident=www-data) by webuniovi.innova.uniovi.es with esmtp (Exim 3.35 #1 (Debian)) id 1A6Z2z-0002Am-00 for ; Mon, 06 Oct 2003 19:21:25 +0200 Date: Mon, 06 Oct 2003 19:25:03 +0200 From: =?UNKNOWN?Q?Rub=E9n?= Meana =?UNKNOWN?Q?Pa=F1eda?= Subject: ECP GAMESS SAPT X-Sender: rubenmp..at..correo.uniovi.es To: chemistry..at..ccl.net Reply-to: rubenmp..at..correo.uniovi.es Message-id: MIME-version: 1.0 X-Mailer: Mailreader.com v2.3.29 (2001-07-20) Content-type: text/plain; charset=iso8859-1 Content-transfer-encoding: 8BIT X-Originating-Host: pcc134.quimica.uniovi.es [156.35.54.35]; Mon, 6 Oct 2003 17:21:25 GMT X-Browser: Mozilla/4.0 (compatible; MSIE 5.0; Windows 95; DigExt), JavaScript: On X-Spam-Status: No, hits=1.1 required=7.0 tests=SUBJ_ALL_CAPS version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I have technical problems with ECP4s and SAPT. I perform SAPT calculations rely on GAMESS. What is the way to be input the ECP data in SAPT? Thanks in advanced to everyone Rubin Meana Paqeda Laboratorio de Qummica Computacional. Dpto de Qummica Fmsica y Analmtica. Facultad de Qummica. Universidad de Oviedo. C/Julian Claverma 8, 332006 Oviedo, Principado de Asturias, Spain e-mail:rubenmp..at..correo.uniovi.es Tel. +985105016 Fax +985237850 From chemistry-request@ccl.net Mon Oct 6 12:50:05 2003 Received: from zmail.pt ([213.13.155.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h96GnV59026077 for ; Mon, 6 Oct 2003 12:49:32 -0400 Received: from WorldClient (authenticated user goncalo.justino..at..zmail.pt) by zmail.pt (MDaemon.PRO.v6.8.4.R) with ESMTP id 23-md50000000010.tmp for ; Mon, 06 Oct 2003 17:46:25 +0100 Received: from [194.117.40.12] via WorldClient with HTTP; Mon, 06 Oct 2003 17:46:24 +0100 Date: Mon, 06 Oct 2003 17:46:24 +0100 From: "=?iso-8859-1?Q?Gon=E7alo?= Deira Justino" To: chemistry..at..ccl.net Subject: AM1, MNDO and PM3 software 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 X-Authenticated-Sender: goncalo.justino..at..zmail.pt X-Spam-Processed: zmail.pt, Mon, 06 Oct 2003 17:46:25 +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=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 CCL, I'm currently using AM1, MNDO and PM3 methods to optimize molecular geometries. Can you tell me any software, preferentially free, but not only, that does this? If it also allows me to get entropy and related stuff, it'd be cool. Thanks Gongalo From chemistry@ccl.net Fri Oct 3 15:54:53 2003 -0400 Return-Path: Subject: Computational Chemistry Grid Conference, Oct. 20-21 2003, Lexington, KY Date: Fri, 3 Oct 2003 15:39:22 -0400 Message-ID: <3DEB727CED850444BC67A65ECB26796A872480|at|ARLABML01.DS.ARL.ARMY.MIL> From: "Zottola, Mark (Cont,ARL/CISD)" To: 3rd Announcement For Computational Chemistry Grid Conference We are pleased to announce the 3rd annual Computational Chemistry Grid Conference sponsored by SURA in collaboration with the National Computational Sciences Alliance (NCSA) , the University of Kentucky and the Department of Defense's Programming Environment and Training (PET) Program to be held at the University of Kentucky in Lexington on October 20 & 21, 2003. The conference will focus on the development and application of techniques in material science, biomolecular modeling/simulation and computational biology. This year our keynote speaker is Dr. Dimitris Papaconstantopoulos from the Naval Research Laboratory. Dr. Papaconstantopoulos is a noted researcher in the field of tight binding methods. In addition, our speaker slate includes: Dr. Thom Dunning, Oak Ridge National Laboratory, Dr. Roger Klein, University of Bonn; Dr. Mary Jo Ondrechen, Northeastern University; Dr. Stephen C. Harvey, Georgia Institute of Technology; and Dr. Theresa Windus, Pacific Northwest National Laboratory. Further information on the conference and the full slate of speakers can be found at http://www.ccs.uky.edu/workshop/SURA2003/ Registration for this conference is free. We will be having a poster session Monday evening, thus submission of posters is highly encouraged. This year we are also proud to announce that through funding from the DOD PET Program, a limited number of travel stipends will be available for students from historically black colleges and universities or minority serving institutions. These stipends will cover airfare and accommodations at the Hyatt Regency in Lexington. An application form is available by going to the SURA website and following the appropriate links. The conference will be webcast using the ACCESS Grid and VRVS technologies. Further information on virtual access for this conference can be be found at http://www.ccs.uky.edu/workshop/SURA2003/ From chemistry-request@ccl.net Mon Oct 6 10:59:09 2003 Received: from llar.net.uniovi.es (llar.net.uniovi.es [156.35.11.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h96Ewa59020745 for ; Mon, 6 Oct 2003 10:58:36 -0400 Received: from CONVERSION-DAEMON.llar.net.uniovi.es by llar.net.uniovi.es (PMDF V6.1 #39514) id <01L1IKUDFGSG012PZK[at]llar.net.uniovi.es> for chemistry[at]ccl.net; Mon, 06 Oct 2003 16:57:43 +0200 (MET) Received: from webuniovi.innova.uniovi.es (webuniovi.innova.uniovi.es [156.35.33.99]) by llar.net.uniovi.es (PMDF V6.1 #39514) with ESMTP id <01L1IKU9WWDS011KVU[at]llar.net.uniovi.es> for chemistry[at]ccl.net; Mon, 06 Oct 2003 16:57:38 +0200 (MET) Received: from localhost ([127.0.0.1] helo=pcc134.quimica.uniovi.es ident=www-data) by webuniovi.innova.uniovi.es with esmtp (Exim 3.35 #1 (Debian)) id 1A6Woj-0000bU-00 for ; Mon, 06 Oct 2003 16:58:33 +0200 Date: Mon, 06 Oct 2003 16:58:54 +0200 From: rubenmp[at]correo.uniovi.es Subject: Problems running CAS using G98 To: chemistry[at]ccl.net Reply-to: rubenmp[at]correo.uniovi.es Message-id: Dear all, While trying to perform a CAS(5,5)/cc-pVQZ calculation using G98 the program does not work properly due to a failure in the algorithm. Attached please find the most relevant information about the calculation, Can I modify the input in such a way that let me perform this calculation? Thanks to everybody Ruben Rubin Meana Paqeda Laboratorio de Qummica Computacional. Dpto de Qummica Fmsica y Analmtica. Facultad de Qummica. Universidad de Oviedo. C/Julian Claverma 8, 332006 Oviedo, Principado de Asturias, Spain e-mail:rubenmp[at]correo.uniovi.es Tel. +985105016 Fax +985237850 ======================================================== Entering Gaussian System, Link 0=g98 Input=casiaddqz.com Output=casiaddqz.log Initial command: /soft/gaussian/g98/l1.exe /scratch/qig0pgb/CBS/Gau-6105.inp -scrdir=/scratch/qig0pgb/CBS/ Entering Link 1 = /soft/gaussian/g98/l1.exe PID= 6106. Copyright (c) 1988,1990,1992,1993,1995,1998 Gaussian, Inc. All Rights Reserved. This is part of the Gaussian(R) 98 program. It is based on the Gaussian 94(TM) system (copyright 1995 Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992 Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990 Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988 Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986 Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983 Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. The following legend is applicable only to US Government contracts under DFARS: RESTRICTED RIGHTS LEGEND Use, duplication or disclosure by the US Government is subject to restrictions as set forth in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFARS 252.227-7013. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA The following legend is applicable only to US Government contracts under FAR: RESTRICTED RIGHTS LEGEND Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraph (c) of the Commercial Computer Software - Restricted Rights clause at FAR 52.227-19. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- Cite this work as: Gaussian 98, Revision A.7, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1998. ***************************************** Gaussian 98: SGI64-G98RevA.7 11-Apr-1999 26-Sep-2003 ***************************************** %mem=750MB %rwf=rut52 %scr=rut52 %nosave %chk=rut52 Default route: MaxDisk=2040MW ---------------------------------------------------------------------- #p CAS(5,5)/cc-pVQZ fopt(calchffc) freq(noraman) IOP(6/7=3) scf(MAxCyc le=400) guess(read,save) geom(allcheck) MAxDisk=20GB ---------------------------------------------------------------------- 1/10=4,18=20,29=7,38=1/1,3; 2/9=110,14=103/2; 3/5=16,6=2,25=1,32=1/1,2,3; 4/5=1,7=6,17=5,18=5/1,5; 5/5=2,7=400,17=1000000/10; 6/7=3,8=2,9=2,10=2,28=1/1; 7/10=1,18=20,25=1/1,2,3,16; 1/10=4,18=20/3(1); 99//99; 2/9=110/2; 3/5=16,6=2,25=1,32=1/1,2,3; 4/5=5,7=6,16=2,17=5,18=5/1; 5/5=2,7=400,17=1000000,23=1,38=4/10; 7//1,2,3,16; 1/18=20/3(-5); 2/9=110/2; 6/7=3,8=2,9=2,10=2,19=2,28=1/1; 99/9=1/99; *************************** 289 basis functions 484 primitive gaussians 17 alpha electrons 16 beta electrons nuclear repulsion energy 72.4637699915 Hartrees. Leave Link 301 at Fri Sep 26 13:15:16 2003, MaxMem= 98304000 cpu: 0.3 *************************** 289 basis functions 484 primitive gaussians 17 alpha electrons 16 beta electrons nuclear repulsion energy 72.4637699915 Hartrees. Leave Link 301 at Fri Sep 26 13:15:16 2003, MaxMem= 98304000 cpu: 0.3 Leave Link 601 at Sat Sep 27 18:47:39 2003, MaxMem= 98304000 cpu: 13.6 (Enter /soft/gaussian/g98/l701.exe) Compute integral second derivatives. ... and contract with generalized density number 0. Density matrix is not symmetric, so symmetry will not be used here. Leave Link 701 at Sat Sep 27 18:48:02 2003, MaxMem= 98304000 cpu: 22.3 (Enter /soft/gaussian/g98/l702.exe) No algorithm selected, NAlg=7. Error termination via Lnk1e in /soft/gaussian/g98/l702.exe. Job cpu time: 1 days 5 hours 23 minutes 43.7 seconds. File lengths (MBytes): RWF= 54 Int= 0 D2E= 0 Chk= 9 Scr= 5