From chemistry-request@server.ccl.net Tue Apr 8 05:12:35 2003 Received: from mail-d.bcc.ac.uk ([144.82.100.24]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h389CYu17834 for ; Tue, 8 Apr 2003 05:12:35 -0400 Received: from mail-e.bcc.ac.uk by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Tue, 8 Apr 2003 10:12:28 +0100 Received: from einstein.chem.ucl.ac.uk (actually host chemc239.chem.ucl.ac.uk) by mail-e.bcc.ac.uk with SMTP (Mailer) with ESMTP; Tue, 8 Apr 2003 10:08:55 +0100 Date: Tue, 8 Apr 2003 10:12:25 +0100 From: Pascal Boulet X-X-Sender: pascal@einstein.chem.ucl.ac.uk Reply-To: P.Boulet@ucl.ac.uk To: =?ks_c_5601-1987?B?vK2w/L/r?= cc: CCL Subject: Re: CCL:option about fixing coordinate of molecule (gaussian) In-Reply-To: <003101c2fd78$2b2f53e0$e325f88f@ilsun> Message-ID: References: <003101c2fd78$2b2f53e0$e325f88f@ilsun> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h389CZu17835 I think it's rather well described in the manual. You can have a look at: http://www.gaussian.com/g_ur/m_molspec.htm and http://www.gaussian.com/g_ur/c_zmat.htm I hope this help, Best Regards, Pascal On Tue, 8 Apr 2003, [ks_c_5601-1987] ¼­°ü¿ë wrote: > Dear all, > > Do you know whether G98 has the option about fixing coordinate of target molecule? > I want to calculate the carbon nanotube using G98 but I can't find this option. > In the case of Dmol3 code, I could find it easily. > To expect your kindness, thank you for reading. > > Regards, > Kwanyong Seo. > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > Kwanyong Seo : (E-mail) cupid@mail.kaist.ac.kr (first) > cupid@kaist.ac.kr > (MSN) chemist_sky@hotmail.com > M.S.candidate > Department of Chemistry > Korea Advanced Institute of Science & Technology > 373-1, Guseong-dong, Yuseong-gu, > Taejon, Republic of Korea > 305-701 > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > -- Dr. Pascal Boulet University College of London Centre for Computational Science Department of Chemistry Gordon Street 20 London, WC1H OAJ UK From chemistry-request@server.ccl.net Tue Apr 8 10:21:16 2003 Received: from antivirus2.its.rochester.edu ([128.151.57.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h38ELGX25430 for ; Tue, 8 Apr 2003 10:21:16 -0400 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with ESMTP id h38ELB4U017526 for ; Tue, 8 Apr 2003 10:21:12 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with SMTP id h38EL4Bv017497 for ; Tue, 8 Apr 2003 10:21:04 -0400 (EDT) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.9/8.12.1) with ESMTP id h38EL2RT002799 for ; Tue, 8 Apr 2003 10:21:03 -0400 (EDT) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: DMSO charmm parameters Date: Tue, 8 Apr 2003 10:18:19 -0400 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200304081018.19404.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h38ELGX25431 Hi, guys: I want to do a simulation of a peptide in DMSO. Can anybody point me to some paper about the parameters of DMSO which I can use? thanks a lot. best regards Wei Zhuang From chemistry-request@server.ccl.net Tue Apr 8 05:02:13 2003 Received: from galadriel.portugalmail.pt ([195.245.179.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3892Cu17637 for ; Tue, 8 Apr 2003 05:02:13 -0400 Received: by galadriel.portugalmail.pt (Postfix on SuSE Linux 7.3 (i386), from userid 65534) id 833E73970B; Tue, 8 Apr 2003 10:02:12 +0100 (WEST) Received: from 193.137.173.132 ( [193.137.173.132]) as user nelson_fonseca@portugalmail.pt@imap.portugalmail.pt by webmail.portugalmail.pt with HTTP; Tue, 8 Apr 2003 10:02:12 +0100 Message-ID: <1049792532.3e9290144577d@webmail.portugalmail.pt> Date: Tue, 8 Apr 2003 10:02:12 +0100 From: nelson_fonseca@portugalmail.pt To: chemistry@ccl.net Subject: Methods and basis sets to study hydrogen bonding MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 193.137.173.132 Dear All I'm trying to perform some electonic calculation in supramolecular systems, and I´m interested in study intermolecular hydrogen bonds between two molecules. Can anyone advice me for the best methods (and basis sets) to study hydrogen bonding? Note that my system is composed of 100 atoms. Thanks Best regards __________________________________________________________ O email preferido dos portugueses agora com 100Mb de espaço e acesso gratuito à Internet http://www.portugalmail.com/gold/ From chemistry-request@server.ccl.net Tue Apr 8 10:43:46 2003 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h38EhkX26144 for ; Tue, 8 Apr 2003 10:43:46 -0400 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 8058A9734; Tue, 8 Apr 2003 16:43:45 +0200 (CEST) To: chemistry@ccl.net Subject: Sybyl atom types Message-ID: <1049813025.3e92e02177585@webmail.u-picardie.fr> Date: Tue, 08 Apr 2003 16:43:45 +0200 (CEST) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, I want to generate .mol2 files automatically in order to use them in insightII for instance... I wonder questions about the sybyl atom types column. I read that "The most common uses of atom types are for molecular mechanics force fields and some property prediction algorithms". Moreover, the sybyl atom type list is described: http://www.tripos.com/custResources/mol2Files/atom_types.html#11465 Could you please tell me exactly in which type of calculations they are used ? Are they use in a the sybyl force field ? Thanks, regards, Francois From chemistry-request@server.ccl.net Tue Apr 8 11:30:45 2003 Received: from exasp.biogeo.uw.edu.pl ([212.87.8.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h38FUiX27489 for ; Tue, 8 Apr 2003 11:30:44 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by exasp.biogeo.uw.edu.pl (Postfix) with ESMTP id 2913215E1F for ; Tue, 8 Apr 2003 17:30:51 +0200 (CEST) Received: by exasp.biogeo.uw.edu.pl (Postfix, from userid 526) id ACC8915E11; Tue, 8 Apr 2003 17:30:49 +0200 (CEST) Date: Tue, 8 Apr 2003 17:30:49 +0200 From: Grzegorz Bakalarski To: CHEMISTRY@ccl.net Subject: g03 on athlon in parallel Message-ID: <20030408153049.GA7819@exasp.biogeo.uw.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i X-Virus-Scanned: by AMaViS snapshot-20020300 Dear CCL Readers, We have two computers: 1) Linux (RH7.3) with 2X Intel Pentium III 1266Mhz procesors 2) Linux (RH7.3) with 2X AMD Athlon 1800+ procesors. We have pgf77 installed and licensed for only Pentium machine. We received G03 and it compiled well on first machine (standard installation). And g03 runs very well on 1 and 2 processors (%nproc=2) I've tried to run executable on second machine, but there was a lack of dynamic libraries. After some modification of i386.make I compiled static version of g03. And it runs quite well on athlon, but only on 1 processor (i.e. %nproc=1) If I sepcify %nproc=2 then I get warning: Warning: OMP_SET_NUM_THREADS greater than available cpus (set to 2; cpus = 1) Warning: OMP_SET_NUM_THREADS greater than NCPUS_MAX, using NCPUS_MAX Will use up to 2 processors via shared memory. Inconsistency in NProc: NTCur= 2 but real number of threads= 1 N= 4 NumPrc= 2 MaxCur= 2 NP= 2. Command exited with non-zero status 1 and g03 stops before reading structure. What is the problem? What means: "real number of threads= 1" ???????????????????????? Should I compile in another way? Are there any setting in Linux I should activate ??? Thanks for any help! Grzegorz From chemistry-request@server.ccl.net Tue Apr 8 11:33:49 2003 Received: from atom.ecn.purdue.edu ([128.46.108.94]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h38FXnX27615 for ; Tue, 8 Apr 2003 11:33:49 -0400 Received: from ecn.purdue.edu (chme117bpc3.ecn.purdue.edu [128.46.108.125]) (authenticated bits=0) by atom.ecn.purdue.edu (8.12.8p1/8.12.8) with ESMTP id h38FXki6015762 for ; Tue, 8 Apr 2003 10:33:46 -0500 (EST) Message-ID: <3E92EBDA.3060208@ecn.purdue.edu> Date: Tue, 08 Apr 2003 10:33:46 -0500 From: Aaron Deskins Organization: Purdue University User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: G98 NMR problem Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned-ECN: by AMaVIS version 11 (perl 5.8) (http://amavis.org/) I am trying to calculate NMR chemical shift values using Gaussian. I have optimized the structure using B3LYP, the VeryTight convergence option for optimization, and the Tight convergence option for the energy, however I get a 5 ppm difference in the shielding tensors predicted for chemically equivalent Si nuclei in the silica dimer. Does anyone have any recommendations as to why I’m seeing such a large difference? Thanks! -- Aaron Deskins Graduate Student Chemical Engineering Purdue University