From chemistry-request@server.ccl.net Mon Aug 6 04:07:34 2001 Received: from mbx.unige.ch ([129.194.8.72]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7687Yv21507 for ; Mon, 6 Aug 2001 04:07:34 -0400 Received: from lcta1 ([129.194.52.184]) by mbx.unige.ch (PMDF V6.0-24 #38753) with SMTP id <0GHM00AODZWLLF@mbx.unige.ch> for chemistry@ccl.net; Mon, 06 Aug 2001 10:07:33 +0200 (MEST) Date: Mon, 06 Aug 2001 10:03:13 +0200 From: Thomas Heine Subject: beyond Verlet's algorithm To: chemistry@ccl.net Reply-to: thomas.heine@chiphy.unige.ch Message-id: <01080610031300.07943@lcta1> Organization: University of Geneva MIME-version: 1.0 X-Mailer: KMail [version 1.1.99] Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8bit Dear CCLers, many MD codes use Verlet's algorithm to obtain trajectories in MD simulations. This algorithm is very compact and optimized for - minimal storage of information - minimal number of operations in the integration process to advance coordinates (and velocities) with time. Let's assume that the computing time needed to get new coordinates R(t+ delta t) is negligible to the time spent for calculating energy and forces. My question is whether there is a more sophisticated algorithm around, which integrates with an as large as possible delta t (determined with some theshold), which uses coordinates, velocities and accelerations of N previous iterations? Thanks in advance Thomas Heine From chemistry-request@server.ccl.net Mon Aug 6 10:18:23 2001 Received: from mail.iitk.ac.in ([203.200.95.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f76EILv29979 for ; Mon, 6 Aug 2001 10:18:22 -0400 Received: from qasid.cc.iitk.ac.in (qasid.cc.iitk.ac.in [172.31.1.16]) by mail.iitk.ac.in (8.9.3+Sun/8.9.2) with ESMTP id TAA19780 for ; Mon, 6 Aug 2001 19:47:20 +0530 (IST) Received: from chinmoy.h1.iitk.ac.in ([172.31.76.193]) by qasid.cc.iitk.ac.in (8.9.2/8.9.2) with ESMTP id TAA14083 for ; Mon, 6 Aug 2001 19:35:38 +0530 (IST) Message-Id: <200108061405.TAA14083@qasid.cc.iitk.ac.in> Subject: problem in install autodock tool kit From: Chinmoy Ranjan To: CHEMISTRY@ccl.net Content-Type: text/plain X-Mailer: Evolution (0.9 - Preview Release) Date: 06 Aug 2001 19:41:21 -0400 Mime-Version: 1.0 Dear CClers, I was trying to install the autodock tool kit for linux platform for python 2.0. While trying to do so I am getting a problem ..... "TOGL not found "?? Any of the user of the tool kit is requuested to tell me how to get around this problem.. I downloaded all the dependent packages from the web site.. ANy help will be appreciated.. bye.. From chemistry-request@server.ccl.net Mon Aug 6 12:20:46 2001 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f76GKjv07216 for ; Mon, 6 Aug 2001 12:20:45 -0400 Received: from szilva by echo.ribotargets.com with local (Exim 3.13 #1) id 15Tn4d-0001Vv-00; Mon, 06 Aug 2001 16:17:47 +0000 Date: Mon, 6 Aug 2001 16:17:47 +0000 From: Szilveszter Juhos To: Chinmoy Ranjan Cc: CHEMISTRY@ccl.net Subject: Re: CCL:problem in install autodock tool kit Message-ID: <20010806161747.D4575@echo.ribotargets.com> References: <200108061405.TAA14083@qasid.cc.iitk.ac.in> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <200108061405.TAA14083@qasid.cc.iitk.ac.in>; from ranjan@iitk.ac.in on Mon, Aug 06, 2001 at 07:41:21PM -0400 On Mon, Aug 06, 2001 at 07:41:21PM -0400, Chinmoy Ranjan wrote: > While trying to do so I am getting a problem > "TOGL not found "?? TOGL is the Tk OpenGL interface (for 3D rendering roughly though TOGL itself provides the graphical user interface stuff not the rendering code). You can find it at https://sourceforge.net/projects/togl/ Hope it helps: Szilva From chemistry-request@server.ccl.net Mon Aug 6 13:15:00 2001 Received: from haney.hbond.com ([207.137.2.252]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f76HEwv07853 for ; Mon, 6 Aug 2001 13:14:59 -0400 Received: (from haney@localhost) by haney.hbond.com (8.9.3/8.9.3) id KAA04234; Mon, 6 Aug 2001 10:17:40 -0700 From: "Dr. David N. Haney" Message-Id: <200108061717.KAA04234@haney.hbond.com> Subject: Molecular Descriptors and Electrostatics Software To: CHEMISTRY@ccl.net Date: Mon, 6 Aug 101 10:17:39 -0700 (PDT) Cc: haney@haney.hbond.com (Dr. David N. Haney) X-Mailer: ELM [version 2.4ME+ PL34 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit eduSoft, LC Announces New Bioinformatic Software: ### MolconnZ TOOLKIT### MolconnZ will be available in a Developers TOOLKIT. This means that MolconnZ's advanced methods for calculating molecular descriptors can be incorporated into your in-house tools, or into tools that you provide to others. Researchers have found MolconnZ's ability to rapidly generate over 300 descriptors invaluable for evaluating their databases of existing compounds as well as their databases of potential new compounds. Use of the MolconnZ molecular descriptors along with database tools, statistical and component analysis provides valuable methods for Bioinformatic Similarity Analysis. ### ZAP ### ZAP is the most rapid and accurate electrostatic calculation program from OpenEye Software, and is provided with an interface to Sybyl by eduSoft. Additional QSAR capabilities for Bioinformatic analysis include surface/volume descriptors, 3D QSAR electrostatic decriptors and binding energies. MolconnZ is also provided by eduSoft with an interface to Sybyl. eduSoft also offers HINT (hydrophobicity) and HASL (3D QSAR model), please visit our website http://www.edusoft-lc.com. Software is available for free trial. VISIT eduSoft and OpenEye Software at the ACS: Aug. 27-29 Booth #265! -- ######### David N. Haney, Ph.D. ######### # Haney Associates Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney@hbond.com # ################# ##################### From chemistry-request@server.ccl.net Mon Aug 6 06:45:45 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f76Ajfv26444 for ; Mon, 6 Aug 2001 06:45:42 -0400 Received: from ppp-212.56.193.74.mldnet.com (ppp-212.56.193.74.mldnet.com [212.56.193.74]) by server.mldnet.com (8.9.3/8.9.3) with ESMTP id NAA00858 for ; Mon, 6 Aug 2001 13:17:27 +0300 Date: Mon, 6 Aug 2001 13:23:04 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <1692991567.20010806132304@yahoo.com> To: chemistry@ccl.net Subject: small molecule activation MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear chemistry, Could anybody give me a reference on recent paper(s) (preferably review) on quantum-chemical investigation of small molecule activation? Thanks. I'll summarize answers. Best regards, Mike mailto:MikePeleah@yahoo.com From chemistry-request@server.ccl.net Mon Aug 6 14:06:04 2001 Received: from hotmail.com ([64.4.19.105]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f76I63v08706 for ; Mon, 6 Aug 2001 14:06:03 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 6 Aug 2001 11:05:57 -0700 Received: from 64.56.138.61 by lw12fd.law12.hotmail.msn.com with HTTP; Mon, 06 Aug 2001 18:05:57 GMT X-Originating-IP: [64.56.138.61] From: "kaci Tizi-Ouzou" To: magneticdolphin@yahoo.com, chemistry@ccl.net, dalton-users@kjemi.uio.no Subject: Re: CCL:MPI libraries for Solaris Date: Mon, 06 Aug 2001 18:05:57 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 06 Aug 2001 18:05:57.0811 (UTC) FILETIME=[71567030:01C11EA2] Greetings, As far as I know, MPI is a specification for messaging passing which allows implementing parallel processing whithout worying about the low level stuff. Two free implementation that I am aware of are: LAM-MPI( Notre Dame University) and MPI-CH (maintained and developed by LANL -Argone Lab-) Both of these packages are free. MPI-CH was also ported to Win32. Hope this helps. Ahmed. >From: Sidney Ramos >To: chemistry@ccl.net, dalton-users@kjemi.uio.no >Subject: CCL:MPI libraries for Solaris >Date: Wed, 1 Aug 2001 07:42:54 -0700 (PDT) > >Dear CCLers and Dalton Users, > >I get the last Dalton 1.2 version and I wish I >compiled the parallel version in the Sun Entreprise(4 >nodes). Anybody knows where can I get MPI libraries >for Solaris? >Thanks for any help! >Best Regards, > >Sidney Ramos >LQTC - DQF - CCEN - UFPE > >__________________________________________________ >Do You Yahoo!? >Make international calls for as low as $.04/minute with Yahoo! Messenger >http://phonecard.yahoo.com/ > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net >70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: >jkl@ccl.net > > > > > _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Mon Aug 6 11:17:49 2001 Received: from sas.asc.hpc.mil ([129.48.244.126]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f76FHnv01063 for ; Mon, 6 Aug 2001 11:17:49 -0400 Received: from asc.hpc.mil (wk32.asc.hpc.mil [129.48.245.32]) by sas.asc.hpc.mil (8.11.5/8.11.5) with ESMTP id f76FHmc116509 for ; Mon, 6 Aug 2001 11:17:48 -0400 (EDT) Sender: duanx@asc.hpc.mil Message-ID: <3B6EB50C.7D4E5202@asc.hpc.mil> Date: Mon, 06 Aug 2001 11:17:33 -0400 From: XIAOFENG FRANK DUAN Organization: CSC X-Mailer: Mozilla 4.76 [en] (X11; U; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Crystal98 and MPI Content-Type: multipart/alternative; boundary="------------7CABA1EF9F198D66F040F7C4" --------------7CABA1EF9F198D66F040F7C4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers: I have been trying to compile a MPI version on our SGI Origin 2000. The compiling was successful, but there was a run-time error (i/o error) if more than one processors were used. I was wondering if somebody here has done so and could give me some advices on it. Thanks! -- Xiaofeng Frank Duan, Ph.D | Phone: 937-904-8307 ASC MSRC | Email: duanx@asc.hpc.mil 2435 5th St., ASC/HP Bldg. 676 | URL: http://www.asc.hpc.mil Wright-Patterson AFB, OH 45433 | --------------7CABA1EF9F198D66F040F7C4 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers:

I have been trying to compile a MPI version on our SGI Origin 2000. The compiling was successful, but there was a run-time error (i/o error) if more than one processors were used. I was wondering if somebody here has  done so and could give me some advices on it.

Thanks! 

-- 
 Xiaofeng Frank Duan, Ph.D         |  Phone: 937-904-8307
 ASC MSRC                          |  Email: duanx@asc.hpc.mil   
 2435 5th St., ASC/HP Bldg. 676    |  URL:   http://www.asc.hpc.mil
 Wright-Patterson AFB, OH 45433    |
  --------------7CABA1EF9F198D66F040F7C4-- From chemistry-request@server.ccl.net Mon Aug 6 02:24:54 2001 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f766Orv08813 for ; Mon, 6 Aug 2001 02:24:53 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.11.2/8.11.2/Guy-12-01-2001) with ESMTP id f766Oqh15224; Mon, 6 Aug 2001 08:24:52 +0200 (METDST) Received: from host5 (host5.lctn.uhp-nancy.fr [193.50.239.5]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with SMTP id IAA20806; Mon, 6 Aug 2001 08:25:52 +0200 Content-Type: text/plain; charset="iso-8859-1" From: Nicolas Ferre Organization: Laboratoire de Chimie Theorique de Nancy To: "De Vito David (DIP)" , "'chemistry@ccl.net'" Subject: Re: CCL:Optimisation with moderedun in Gaussian 98 Date: Mon, 6 Aug 2001 08:14:41 +0200 X-Mailer: KMail [version 1.2] References: In-Reply-To: MIME-Version: 1.0 Message-Id: <0108060814410P.16254@host5> Content-Transfer-Encoding: 8bit Hi David, This is not the first time I see this request for partial optimization, given the input geometry in cartesian coordinates (CCL archives !!) You don't need to use ADDREDUNDANT. Between the atomic symbol and the coordinates, write 0 to let the atom moving freely (this is the default) or write -1 to freeze its position. Your input would be: # BP86 OPT GEN Pseudo=Read Optimisation of Ir(H2O)6 GS 3 1 Ir 0 0.0000000000 0.0000000000 0.0000000000 O 0 -2.0789600000 0.0000000000 0.0000000000 O 0 2.0789600000 0.0000000000 0.0000000000 O 0 0.0000000000 -2.0789600000 0.0000000000 O 0 0.0000000000 2.0789600000 0.0000000000 O 0 0.0000000000 0.0000000000 -2.0789600000 O -1 0.0000000000 0.0000000000 2.0789600000 H 0 -2.6297790000 0.0000000000 0.8244590000 H 0 2.6297790000 0.0000000000 -0.8244590000 H 0 -2.6297790000 0.0000000000 -0.8244590000 H 0 2.6297790000 0.0000000000 0.8244590000 H 0 -0.8244590000 -2.6297790000 0.0000000000 H 0 0.8244590000 -2.6297790000 0.0000000000 H 0 -0.8244590000 2.6297790000 0.0000000000 H 0 0.8244590000 2.6297790000 0.0000000000 H -1 0.0000000000 -0.8244590000 2.6297790000 H 0 0.0000000000 0.8244590000 -2.6297790000 H 0 0.0000000000 -0.8244590000 -2.6297790000 H -1 0.0000000000 0.8244590000 2.6297790000 Nicolas On Sunday 05 August 2001 07:48, De Vito David (DIP) wrote: > Good morning from Switzerland ! > > I'm trying to make optimisation with cartesian coordinates with Gaussian > 98. I'd like to keep some atoms freezed in the molecule and I use the > AddRedun mode to make this. > > The first optimisation cycle seems to work fine, but after, all the atoms > coordinates are modified and at the end of optimisation, the atoms that I > frozed are displaced too. > > Here is my input, I hope that somebody can help me ! > > > Best regards, > > > D. De Vito. > > > ----------------------------------------------------- > > > # BP86 OPT=AddRedun GEN Pseudo=Read > > Optimisation of Ir(H2O)6 GS > > 3 1 > Ir 0.0000000000 0.0000000000 0.0000000000 > O -2.0789600000 0.0000000000 0.0000000000 > O 2.0789600000 0.0000000000 0.0000000000 > O 0.0000000000 -2.0789600000 0.0000000000 > O 0.0000000000 2.0789600000 0.0000000000 > O 0.0000000000 0.0000000000 -2.0789600000 > O 0.0000000000 0.0000000000 2.0789600000 > H -2.6297790000 0.0000000000 0.8244590000 > H 2.6297790000 0.0000000000 -0.8244590000 > H -2.6297790000 0.0000000000 -0.8244590000 > H 2.6297790000 0.0000000000 0.8244590000 > H -0.8244590000 -2.6297790000 0.0000000000 > H 0.8244590000 -2.6297790000 0.0000000000 > H -0.8244590000 2.6297790000 0.0000000000 > H 0.8244590000 2.6297790000 0.0000000000 > H 0.0000000000 -0.8244590000 2.6297790000 > H 0.0000000000 0.8244590000 -2.6297790000 > H 0.0000000000 -0.8244590000 -2.6297790000 > H 0.0000000000 0.8244590000 2.6297790000 > > 1 B > 2 B > 3 B > 4 B > 5 B > 6 B > 7 B > 8 B > 9 B > 10 B > 11 B > 12 B > 13 B > 14 B > 15 B > 16 B > 17 B > 18 B > 19 B > 7 F > 16 F > 19 F > > >... > > **************************************************************** > > D. De Vito > Enseignant de Chimie et d'Informatique, Bureau de Gestion > Collège Rousseau > 16A, Avenue du Bouchet > Case Postale 216 > 1211 Genève 28 > Suisse > +4122 / 733.71.30 (Collège) > +4122 / 328.92.16 (Domicile) > +4176 / 532.47.40 (Mobile) > http://lcta.unige.ch/~devito (Personal Page) > http://wwwedu.ge.ch/po/rousseau (Site Officiel du Collège) > > **************************************************************** > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net -- Nicolas FERRE Equipe de Chimie Theorique - UMR UHP/CNRS 7565 BP 139 - 54506 VANDOEUVRE-LES-NANCY - FRANCE Phone: +33 3 83 91 20 00 (ask for 35 52) Fax : +33 3 83 91 25 30 http://www.lctn.uhp-nancy.fr/Etudiants/Nicolas.Ferre.html