From chemistry-request@ccl.net Thu Nov 11 14:01:04 2004 Received: from mail-h12-03.cc.ksu.edu (mail-h12-03.cc.ksu.edu [129.130.12.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iABJ12Pw030840 for ; Thu, 11 Nov 2004 14:01:03 -0500 Received: from ksu.edu ([129.130.170.55]) by mail-h12-03.cc.ksu.edu (8.12.9/8.12.9) with ESMTP id iABJEX0g026984 for ; Thu, 11 Nov 2004 13:14:37 -0600 (CST) Message-ID: <4193BA19.5080104~at~ksu.edu> Date: Thu, 11 Nov 2004 13:14:33 -0600 From: Gustavo Seabra User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030225 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY~at~ccl.net Subject: CCL: G03 with Fedora? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: ClamAV 0.80/585/Thu Nov 11 06:22:42 2004 clamav-milter version 0.80j on virusfilter2.cc.ksu.edu X-Virus-Status: Clean X-Spam-Status: No, hits=3.0 required=7.5 tests=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 Hi, I just wonder if anyone has any experience installing Gaussian 03 in any version of Fedora Core. We are about to intall Fedora Core 3, but I'd like to be sure Gaussian would run there first. Thanks, -- ------------------------------------------------------------------------ *Gustavo Seabra* - Graduate Student E-Mail: seabra~at~ksu.edu Phone: (785) 532-6072 Chemistry Department Kansas State University Manhattan, KS 66506-3701 From chemistry-request@ccl.net Thu Nov 11 15:28:21 2004 Received: from pernis.its.uu.se (pernis.its.UU.SE [130.238.4.153]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iABKSIPw004999 for ; Thu, 11 Nov 2004 15:28:19 -0500 Received: by pernis.its.uu.se (Postfix, from userid 205) id C830E227; Thu, 11 Nov 2004 21:41:53 +0100 (MEZ) Received: from pernis.its.uu.se(127.0.0.1) by pernis.its.uu.se via virus-scan id s335; Thu, 11 Nov 04 21:41:48 +0100 Received: from xray.bmc.uu.se (xray.bmc.uu.se [130.238.41.195]) by pernis.its.uu.se (Postfix) with ESMTP id 19F8114B; Thu, 11 Nov 2004 21:41:47 +0100 (MEZ) Received: from rembrandt.bmc.uu.se (rembrandt.bmc.uu.se [130.238.41.202]) by xray.bmc.uu.se (Postfix) with ESMTP id C7BEA2507B; Thu, 11 Nov 2004 21:41:47 +0100 (CET) Date: Thu, 11 Nov 2004 21:41:47 +0100 (CET) From: David van der Spoel X-X-Sender: spoel-.at.-rembrandt.bmc.uu.se To: Gustavo Seabra Cc: CHEMISTRY-.at.-ccl.net Subject: Re: CCL:G03 with Fedora? In-Reply-To: <4193BA19.5080104-.at.-ksu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.1 required=7.5 tests=RM_fw_FromIsPhras2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Thu, 11 Nov 2004, Gustavo Seabra wrote: >Hi, > >I just wonder if anyone has any experience installing Gaussian 03 in any > version of Fedora Core. We are about to intall Fedora Core 3, but I'd >like to be sure Gaussian would run there first. I have it running on Fedora 3 on Athlon 64, you need RHEL to compile it though (since the compiler only works there). The athlon is not very stable, but that is probably due to the disk. > >Thanks, > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel-.at.-xray.bmc.uu.se spoel-.at.-gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@ccl.net Wed Nov 10 17:35:27 2004 Received: from web53908.mail.yahoo.com (web53908.mail.yahoo.com [206.190.36.218]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAAMZQAQ008576 for ; Wed, 10 Nov 2004 17:35:26 -0500 Received: (qmail 25652 invoked by uid 60001); 10 Nov 2004 22:48:08 -0000 Comment: DomainKeys? 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IECMD 2004 covers all areas of molecular design and uses the Internet for exchanging information. All discussions of the IECMD 2004 papers will take place on the Web, using the Yahoo! group iecmd2004. Please visit the IECMD 2004 discussion site at http://groups.yahoo.com/group/iecmd2004 to sign-up and send comments to the group. There will be no registration for visitors of IECMD 2004, and all PDF papers will be free for download. After the Conference, all accepted papers will be published in IEJMD - the Internet Electronic Journal of Molecular Design, http://www.biochempress.com. 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Front Page. www.yahoo.com From chemistry-request@ccl.net Thu Nov 11 07:37:19 2004 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iABCbEX4007539 for ; Thu, 11 Nov 2004 07:37:15 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2655.55) id ; Thu, 11 Nov 2004 10:49:31 -0300 Message-ID: <4DB0991764FED5119A2A000475B057CA1C5898|at|correio.cetem.gov.br> From: Ian Hovell To: "'chemistry'" Subject: CCL: Summary: Integration grid defaulting to unpruned value Date: Thu, 11 Nov 2004 10:49:22 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4C7F5.3F9A0570" X-Spam-Status: No, hits=2.0 required=7.5 tests=HTML_FONTCOLOR_UNKNOWN, HTML_MESSAGE,LINES_OF_YELLING 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 message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C4C7F5.3F9A0570 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Many thanks. My original question was =20 I am calculating the heats of reactions containing organo-mercury = compounds. I am using G03 and DFT methods. The program, when mercury is involved, defaults to an unpruned integration grid for this atom. The manual = states that one should use the same grid when comparing energies. Does this = mean that I should be defining an unpruned grid for all of my calculations = i.e. the compounds without mercury in the isodesmic reaction? If so how do I define an unpruned grid the same as the one being used by gaussian when mercury is involved. The manual does not talk about unpruned grids. I = have enclosed the relevant output section below.=20 And the replies:- =20 Only the mercury atom will use the unpruned grid. All the other atoms will use the default, pruned grid if it is defined. =20 So you need not do anything special in generating the pieces of the reaction. Each element will be done the same way if you use the defaults in Gaussian. =20 The point of printing the informational message is in the event that you compare with another program or a future release of Gaussian were a pruned grid for mercury might be used. Douglas J. Fox Technical Support Gaussian, Inc. =20 fox|at|gaussian.com =20 =20 I think the manual is referring to using different grid densities, that is, INT=3DULTRAFINE versus INT=3DFINE. A pruned grid has some of the = points removed (hence the word 'pruned') so it is faster, but it should give the same result as an unpruned grid, for the same integration grid density. =20 To summarise, I think you don't need to worry about the pruned grid, so long as you use the same integration grid density (for example, the default integration grid density) for all calculations. =20 Regards, Noel =20 =20 Ian Hovell - Ph.D.=20 NUCLEO DE MODELAGEM MOLECULAR-NMM=20 Centro de Tecnologia Mineral - CETEM=20 Ministerio da Ci=EAncia e da Tecnologia- MCT=20 Avenida Ip=EA, No 900 - Cidade Universitaria=20 Ilha do Fund=E3o Rio de Janeiro RJ Brasil=20 CEP 21941-590=20 tel 00 55 (xx) 3865 7344 ou 3865 - 7216=20 Fax 00 55 (xx) 22602837 ou 2290-4286=20 e-mail hovell|at|cetem.gov.br =20 ------_=_NextPart_001_01C4C7F5.3F9A0570 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Many thanks.

My original question was

 

=

I am calculating the heats of reactions = containing organo-mercury compounds. I am using G03 and DFT methods. The program, = when mercury is involved, defaults to an unpruned integration grid for this = atom. The manual states that one should use the same grid when comparing = energies. Does this mean that I should be defining an unpruned grid for all of my calculations i.e. the compounds without mercury in the isodesmic = reaction? If so how do I define an unpruned grid the same as the one being used by = gaussian when mercury is involved. The manual does not talk about unpruned = grids. I have enclosed the relevant output section below. =

And the replies:-

 

=

   Only the mercury atom = will use the unpruned grid.  All = the other

atoms = will use the default, pruned grid if it is defined.

 

   So you need not do = anything special in generating the pieces of

the reaction.  Each element = will be done the same way if you use

the = defaults in Gaussian.

 

   The point of printing = the informational message is in the event that

you = compare with another program or a future release of Gaussian were

a pruned = grid for mercury might be used.

Douglas = J. Fox

Technical Support

Gaussian, = Inc.

 

fox|at|gaussian.com=

 

 

I think = the manual is referring to using different grid densities, = that

is, INT=3DULTRAFINE versus INT=3DFINE. A pruned grid has some of the = points

removed = (hence the word 'pruned') so it is faster, but it should = give

the same = result as an unpruned grid, for the same integration grid

density.

 

To = summarise, I think you don't need to worry about the pruned grid, = so

long as = you use the same integration grid density (for example, the

default integration grid density) for all calculations.

 

Regards,=

Noel

 

=

 

=

<= font color=3Dblack>Ian = Hovell - Ph.D.

NUCLEO = DE MODELAGEM MOLECULAR-NMM

Centro de Tecnologia Mineral - CETEM

Ministerio da Ci=EAncia e da Tecnologia- MCT

Avenida Ip=EA, No 900 - Cidade Universitaria

Ilha do Fund=E3o Rio de Janeiro RJ Brasil

CEP 21941-590

tel 00 55 (xx) 3865 7344 ou 3865 - 7216

Fax 00 55 (xx) 22602837 ou 2290-4286 <= o:p>

e-mail hovell|at|cetem.gov.br

 =

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