From chemistry-request@ccl.net Mon Jun 23 09:18:44 2003 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5NDIe5u023091 for ; Mon, 23 Jun 2003 09:18:42 -0400 Received: from fen.bilkent.edu.tr (fenII-124.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.12.8/8.12.8) with ESMTP id h5NDCbQn027571 for ; Mon, 23 Jun 2003 16:12:38 +0300 (EET DST) Message-ID: <3EF6FF39.7070803{at}fen.bilkent.edu.tr> Date: Mon, 23 Jun 2003 16:23:05 +0300 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry Subject: CCL: TDHF Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, the time-dependent Hartree-Fock method is described as a method for calculating excited states. I would like to know whether one can also optimize the ground state including correlation with TDHF. In other words, if I use the keywords "fopt" and "nroot=0" in Gaussian what am I calculating? I know that CIS does not make a correction to the ground state because of Brillouin's theorem but I am not sure what TDHF includes exactly. The reason why I am considering this is that I would like to compare the excitet state and the ground state geometries on equal footing. Would it be better to compare the excited state TDHF geometry to the HF ground state geometry? Thanks in advance, Ulrike Salzner From chemistry-request@ccl.net Mon Jun 23 15:06:28 2003 Received: from bfp.cc.purdue.edu (bfp.cc.purdue.edu [128.210.189.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5NJ6S5u002380 for ; Mon, 23 Jun 2003 15:06:28 -0400 Received: from bfp.cc.purdue.edu (localhost [127.0.0.1]) by bfp.cc.purdue.edu (8.12.9/8.12.9) with ESMTP id h5NJ6Obi007322 for ; Mon, 23 Jun 2003 14:06:24 -0500 (EST) Received: from localhost (bfp@localhost) by bfp.cc.purdue.edu (8.12.9/8.12.9/Submit) with ESMTP id h5NJ6OPm007319 for ; Mon, 23 Jun 2003 14:06:24 -0500 (EST) X-Authentication-Warning: bfp.cc.purdue.edu: bfp owned process doing -bs Date: Mon, 23 Jun 2003 14:06:23 -0500 (EST) From: Bryan Putnam X-X-Sender: bfp_at_bfp.cc.purdue.edu To: CCL Subject: Re: g03 and RedHat 7.3 on Pentium In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks for all the responses I got to this question. I found out from Gaussian, Inc. that there is a patched version of libpgthread.so that can be downloaded from the Portland group ftp server (ftp.pgroup.com), which addresses this problem with RedHat 7.3. And yes, you also need to modify the g03.make to remove Pentium IV specific options, if you have for example, a PIII. Thanks, Bryan On Sun, 22 Jun 2003, Bryan Putnam wrote: > Greetings, > > Has anyone had success building Gaussian 03 (g03-B.03) on a Pentium II or > III, using RedHat Linux 7.3, and Portland Group compiler 4.0-2 ? > > I see in the installation notes that Gaussian, Inc. says it will "NOT > work" with versions of RedHat earlier than 8.0, but I don't know if that's > the issue or not. > > g03 seems to compile OK, but when the build gets to the point where the > executables are linked, for example, > > pgf77 -mp -O2 -tp p7 -Mreentrant -Mrecursive -Mnosave -Minfo \ > -Mneginfo -time -fast -Munroll \ > -Mvect=assoc,recog,cachesize:524288,prefetch,sse \ > -fastsse -Mscalarsse -g -o g03 ml0.o util.so -lm -lc > > I get many undefined references of the form, > > /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_msync@GLIBC_2.0' > > I've reproduced the entire horrible list of them below. I've tried various > things, building statically, dynamically, adding additional libraries, > using the Portland version of pgcc, trying various versions of gcc, etc., > but nothing seems to work. > > Any help or suggestions appreciated! > > Thanks, > Bryan > From chemistry-request@ccl.net Mon Jun 23 06:51:52 2003 Received: from typhoeus.chem.york.ac.uk (typhoeus.chem.york.ac.uk [144.32.72.225]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5NApp5u013711 for ; Mon, 23 Jun 2003 06:51:52 -0400 Received: from ysbl.york.ac.uk (onion [144.32.72.165]) by typhoeus.chem.york.ac.uk (8.12.8/8.12.8) with ESMTP id h5NAppUD017371 for ; Mon, 23 Jun 2003 11:51:51 +0100 (BST) Sender: chandra_at_typhoeus.chem.york.ac.uk Message-ID: <3EF6DBC7.B051BA52_at_ysbl.york.ac.uk> Date: Mon, 23 Jun 2003 11:51:51 +0100 From: Chandra Verma X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: Help Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi I am trying to get a set of charges (Mulliken analysis) on a system that has two Nickel atoms that are coordinated to various residues in a a protein, using GAMESS. I would appreciate any help on the kinds of basis sets that ought to be used.... thanks chandra From chemistry-request@ccl.net Mon Jun 23 02:48:05 2003 Received: from mbu.iisc.ernet.in (mbu.iisc.ernet.in [144.16.74.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5N6m05u001478 for ; Mon, 23 Jun 2003 02:48:04 -0400 Received: from mbu.iisc.ernet.in (localhost.localdomain [127.0.0.1]) by mbu.iisc.ernet.in (8.12.8/8.12.5) with ESMTP id h5N7QeiB027768; Mon, 23 Jun 2003 12:56:40 +0530 Received: from localhost (gyan@localhost) by mbu.iisc.ernet.in (8.12.8/8.12.5/Submit) with ESMTP id h5N7QUGL027743; Mon, 23 Jun 2003 12:56:37 +0530 Date: Mon, 23 Jun 2003 12:56:30 +0530 (IST) From: Gyanendra kumar To: =?gb2312?q?Jinsong=20Zhao?= cc: CCL Subject: Re: CCL:AIMPAC running with gcc 3.2 or higher In-Reply-To: <20030622122158.77636.qmail:at:web15214.mail.bjs.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Though I have not used AIMPAC, but while using Autodock, I faced the problem of "Segmentation fault" which could be sorted out by setting the stacksize unlimited in ur .bashrc or .cshrc file. ulimit -s unlimited try this. Gyan. file On Sun, 22 Jun 2003, [gb2312] Jinsong Zhao wrote: > Dear all, > > Does anyone here have a version of AIMPAC (source > code) that could be run under RH8.0 with gcc 3.2 or > higher? > > I have gotten very kindly help from Dr. Jeffrey D. > Saxe and Dr. Julia Metzker concerning AIMPAC codes. > There are no any errors when I compiled them, but when > I run it, I got "segmentation fault". I was told it > may due to I have a higher version of gcc. > > Does anyone here have the similar experience, and > what's your solutions? > > Any help will be very appreciated. > > Thanks in advance. > > Regards, > > Jinsong > > _________________________________________________________ > Do You Yahoo!? > MxA55DZ9JM#:UfGi;9JG7EW]#? > http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/netlove > > > -= This is automatically added to each message by 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > -- ******************************************** Gyanendra Kumar (Research Student), Prof. A. Surolia's Lab, #204, Molecular Biophysics Unit, Indian Institute Of Science, Bangalore, PIN-560012.INDIA, Phone 91-80-293-2389,-2714(Lab), -2539(Res). http://mbu.iisc.ernet.in/~surolia/gyan.html ******************************************** Residence: R-17, Students Hostel, IISc. ******************************************** From chemistry-request@ccl.net Mon Jun 23 03:06:34 2003 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5N76R5u001787 for ; Mon, 23 Jun 2003 03:06:33 -0400 Received: from fen.bilkent.edu.tr (fenII-124.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.12.8/8.12.8) with ESMTP id h5N703Qn015350 for ; Mon, 23 Jun 2003 10:00:10 +0300 (EET DST) Message-ID: <3EF6A7E8.80208=at=fen.bilkent.edu.tr> Date: Mon, 23 Jun 2003 10:10:32 +0300 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry=at=ccl.net Subject: TDHF Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, the time-dependent Hartree-Fock method is described as a method for calculating excited states. I would like to know whether one can also optimize the ground state including correlation with TDHF. In other words, if I use the keywords "fopt" and "nroot=0" in Gaussian what am I calculating? I know that CIS does not make a correction to the ground state because of Brillouin's theorem but I am not sure what TDHF includes exactly. The reason why I am considering this is that I would like to compare the excitet state and the ground state geometries on equal footing. Would it be better to compare the excited state TDHF geometry to the HF ground state geometry? Thanks in advance, Ulrike Salzner From chemistry-request@ccl.net Sun Jun 22 23:54:07 2003 Received: from web15203.mail.bjs.yahoo.com (web15203.mail.bjs.yahoo.com [202.3.77.133]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h5N3s55u031400 for ; Sun, 22 Jun 2003 23:54:06 -0400 Message-ID: <20030623035401.67306.qmail_at_web15203.mail.bjs.yahoo.com> Received: from [218.30.18.116] by web15203.mail.bjs.yahoo.com via HTTP; Mon, 23 Jun 2003 11:54:01 CST Date: Mon, 23 Jun 2003 11:54:01 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: How to calculate the Hammett parameter? To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, Is there a method or program to calculate the Hammett parameter which is used in organic chemistry to describe the electronic properties of molecules. I will appreciate any response and suggestions. Thanks in advance! Regards, Jinsong _________________________________________________________ Do You Yahoo!? MxA55DZ9JM#:UfGi;9JG7EW]#? http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/netlove