From alexei@palladium.enscm.fr Thu Jun 11 03:12:40 1998 Received: from palladium.enscm.fr (palladium.enscm.fr [193.52.207.107]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA15186 Thu, 11 Jun 1998 03:12:38 -0400 (EDT) Received: from localhost (alexei@localhost) by palladium.enscm.fr (8.8.7/8.8.7) with SMTP id JAA19988; Thu, 11 Jun 1998 09:07:39 +0200 (MDT) Date: Thu, 11 Jun 1998 09:07:38 +0200 (MDT) From: Arbouznikov Alexei X-Sender: alexei@palladium To: CHEMISTRY@www.ccl.net cc: CHEMISTRY@www.ccl.net Subject: frustrated translations In-Reply-To: <199806090058.JAA08500@deews1.dent.okayama-u.ac.jp> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, I would be very much obliged to anybody who could give me references on the following problem: It is known that a molecule, after being adsorbed on a solid surface, loses its translational (and rotational - if it is not a monoatomic one) degrees of freedom. One of the translations is transformed into vibration against the adsorption site (and usually correlates very well with the adsorption energy). Two other translations are transformed to vibrations also, but the latter are the displacements in the plane of the surface. There are experimental measurements of these "frustrated translations" (e.g., by J.T.Yates, Jr. et el.). However, I failed to find any THEORETICAL SIMULATIONS of these motions. Any hint will be greatly appreciated. At the moment, it even doesn't matter for me, which molecules on which surface are adsorbed. Summary is guaranteed. Regards, Dr. Alexei Arbouznikov Ecole Nationale Superieure de Chimie, Laboratoire de Materiaux Catalytiques et Catalyse en Chimie Organique, UMR 5618 CNRS-ENSCM - Prof. F.Fajula, 8, rue de l'Ecole Normale 34296 Montpellier, Cedex 5 FRANCE Telephone: (33) 4-67-14-72-68 Fax: (33) 4-67-14-43-49 E-mail: alexei@palladium.enscm.fr From Laurent.PETITJEAN@CALDCRD.elf-atochem.fr Thu Jun 11 06:54:40 1998 Received: from xr1-gw.atlas.fr (xr1-a.atlas.fr [194.51.9.17]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA15860 Thu, 11 Jun 1998 06:54:39 -0400 (EDT) Message-Id: <199806111054.GAA15860@www.ccl.net> X400-Received: by /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Thu, 11 Jun 1998 12:54:24 +0200 X400-Received: by mta xr1-gw.atlas.fr in /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Thu, 11 Jun 1998 12:54:24 +0200 X400-Received: by /ADMD=ATLAS/C=FR/; Relayed; Thu, 11 Jun 1998 12:54:26 +0200 X400-Received: by /PRMD=ELF03/ADMD=ATLAS/C=FR/; Relayed; Thu, 11 Jun 1998 15:49:59 +0200 Date: Thu, 11 Jun 1998 15:49:59 +0200 X400-Originator: Laurent.PETITJEAN@CALDCRD.elf-atochem.fr X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=ELF03/ADMD=ATLAS/C=FR/;980611134959] X400-Content-Type: P2-1984 (2) Content-Identifier: CSI NC V3.0 From: PETITJEAN Laurent GRL To: "'Computational Chemistry List '" (Receipt Notification Requested) (Non Receipt Notification Requested) Subject: G94 error mlessage Dear CCLers, I run several G94 calculations on an origin 2000 SGI server and some jobs stop without reasons. I just get this message : > Erroneous write. write -1 instead of 4096 > Write error in NtrExt1 I just wanted to know if someone among the CCL know how to turn around this problem. L. Petitjean Groupement de Recherche de Lacq B.P. 34 64170 ARTIX tel : 33 5 59 92 67 34 fax : 33 5 59 92 67 65 e-mail : laurent.petitjean@caldcrd.elf-atochem.fr From amartinez@cesca.es Thu Jun 11 04:17:07 1998 Received: from prades.cesca.es (root@prades.cesca.es [192.94.163.152]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA15429 Thu, 11 Jun 1998 04:17:04 -0400 (EDT) Received: from montsia.cesca.es (montsia.cesca.es [192.94.163.137]) by prades.cesca.es (8.8.5/8.8.5) with SMTP id KAA31694 for ; Thu, 11 Jun 1998 10:14:10 +0200 Date: Thu, 11 Jun 1998 10:19:27 +0200 (MDT) From: Alicia Martinez-Puebla To: chemistry@www.ccl.net Subject: Barcelona, July 9th, Seminar on ADF Applications Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 1896 Seminar on ADF applications --------------------------- CESCA - Barcelona, July 9th 1998 (Centre for Supercomputation of Catalonia) This seminar is addressed to researchers and postgraduates who use Quantum Chemistry tools as a help to their current research, and want to have a closer look at the possibilities that the ADF program (Amsterdam Density Functional) offers as a DFT implementation. 9:00- 9:50 Elementary concepts of chemical bonding and analysis tools in ADF Prof. Evert J. Baerends (Vrije Universiteit, Amsterdam) 10:00-10:30 Differences between DFT implementation in Gaussian and ADF (wavefunction, numerical integration, charge analysis) Dr. Miquel Sola (UdG) 10:30-11:00 Pause 11:00-11:30 Metal-ligand bonding in mono- and dinuclear TM complexes Prof. Evert J. Baerends (Vrije Universiteit, Amsterdam) 11:30-12:00 Brief discussion on parallelization and propierty evaluation Prof. Evert J. Baerends (Vrije Universiteit, Amsterdam) 12:10-13:20 The experience of users (I) Dr. Vicenc, Branchadell (UAB) Dr. Miquel Sola (UdG) 13:20-15:20 Lunch 15:20-16:30 The experience of users (II) Mr. Jordi Munyoz (URV) Mr. Jordi Vazquez (UB) 16:30-18:30 Implementation of ADF at CESCA: hands-on Mrs. Alicia Martinez, Ms. Ingrid Barcena (CESCA) Where: Conference Room CESCA ('Annexus' Building) Gran Capita s/n 08034 Barcelona (Spain) Seats: Limited to 40 For more information please contact Ms. Clara Torreblanca (phone: 34-93-205 64 64, fax: 34-93-205 69 79, e-mail: clara@cesca.es) or consult the web page http://www.cesca.es/esp/formacion/congresos.html From yfzhai@iris3.shmm.ac.cn Thu Jun 11 03:32:56 1998 Return-Path: Received: from iris3.shmm.ac.cn ([202.127.19.43]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA15311 Thu, 11 Jun 1998 03:32:50 -0400 (EDT) Received: by iris3.shmm.ac.cn (931110.SGI/940406.SGI.AUTO) for chemistry-request@www.ccl.net id AA10840; Sun, 11 Jun 95 15:20:22 -0700 Date: Sun, 11 Jun 95 15:20:22 -0700 From: yfzhai@iris3.shmm.ac.cn (Yufeng Zhai) Message-Id: <9506112220.AA10840@iris3.shmm.ac.cn> To: chemistry-request@www.ccl.net Subject: Need Help Dear sir, I met a problem in calculating systems containing metal Rh. When Lanl2dz basis set is used with B3LYP method, a line No unpruned grid is available for this atom will appear in the output file, when HF method is used , this information will not be printed in the output file. Could you tell me what the line No unpruned grid is available for this atom means and whether the B3LYP method is proper for the metal Rh. By the way, could you tell me at which level and which method the geometries optimized are good for Rh when time cost is as little as possible. My e-mail address is yfzhai@iris3.shmm.ac.cn Thank you in advance. Yous sincerely Yufeng Zhai From chas@alinga.newcastle.edu.au Thu Jun 11 18:34:46 1998 Received: from alinga.newcastle.edu.au (chas@alinga.newcastle.edu.au [134.148.160.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA21017 Thu, 11 Jun 1998 18:34:43 -0400 (EDT) Received: from localhost (chas@localhost) by alinga.newcastle.edu.au (8.8.5/8.8.5) with SMTP id IAA23412; Fri, 12 Jun 1998 08:34:33 +1000 (EST) Date: Fri, 12 Jun 1998 08:34:33 +1000 (EST) From: SUDARKO A To: PETITJEAN Laurent GRL cc: "'Computational Chemistry List '" Subject: Re: CCL:G:G94 error mlessage In-Reply-To: <199806111054.GAA15860@www.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 11 Jun 1998, PETITJEAN Laurent GRL wrote: > > Dear CCLers, > > I run several G94 calculations on an origin 2000 SGI server and some jobs > stop without reasons. I just get this message : > > > Erroneous write. write -1 instead of 4096 > > Write error in NtrExt1 > That means you run out disk space for your scrath file. Cheers, *************************************************************************** Sudarko 4/19 Gamack ST Chemistry Department Mayfield NSW 2304 The University of Newcastle Tel : (H) (+)61-2-49688382 Callaghan NSW 2308 (O) (+)61-2-49215467 From tapas@risky3.thchem.siu.edu Thu Jun 11 19:09:26 1998 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA21182 Thu, 11 Jun 1998 19:09:25 -0400 (EDT) Received: (from tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) id SAA21278; Thu, 11 Jun 1998 18:14:30 -0500 (CDT) Date: Thu, 11 Jun 1998 18:14:29 -0500 (CDT) From: Tapas Kar To: ComputerChemistryList Subject: References on 1H NMR (Theory and Expt) studies on H-bond Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am looking for 1H NMR studies (theoretical as well as experimental papers/reviews) on H-bonded systems. Tapas tapas@risky3.thchem.siu.edu ----------------- Tapas Kar, Ph. D Asst. Scientist Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433 From dek@sun-ra.ucsf.edu Tue Jun 9 10:57:25 1998 Received: from cgl.ucsf.EDU (cgl.ucsf.EDU [128.218.27.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA02626 Tue, 9 Jun 1998 10:57:24 -0400 (EDT) Received: from sun-ra.ucsf.edu (root@sun-ra.ucsf.EDU [128.218.22.43]) by cgl.ucsf.EDU (8.8.7/GSC4.26) with ESMTP id HAA19942; Tue, 9 Jun 1998 07:57:16 -0700 (PDT) Received: from sun-ra.ucsf.edu ([127.0.0.1]) by sun-ra.ucsf.edu with esmtp (ident dek using rfc1413) id m0yjPoW-000WN7C (Debian Smail-3.2 1996-Jul-4 #2); Tue, 9 Jun 1998 07:55:52 -0700 (PDT) Message-Id: Reply-To: dek@cgl.ucsf.EDU To: chemistry@www.ccl.net Subject: Re: CCL:Re: fortran Compiler for Linux Box. Options? In-reply-to: Your message of "Mon, 08 Jun 1998 10:40:54 EDT." Date: Tue, 09 Jun 1998 07:55:52 -0700 From: David Konerding "William T. Rankin" writes: >> I am willing to go freeware, but I would spend the money on >> a good Fortran compiler to gain the performance. (I also believe >> there is no freeware fortran compiler for f90 code!) > >I picked up some information form The Portland Group, who markets >auto-parallelizing FORTRAN compilers for Linux. You may want to >look them up at http://www.pgroup.com/ > >Now having said that, I will point out that even with the best >tools, simply running a compiler over existing serial FORTRAN >codes will most likely not produce highly scalable parallel code >without some sort of programmer direction from within the source. Hi- I've used both g77 the Portland Group compiler for AMBER 5.0 both with and without MPI (message passing interface). I've had excellent results using Portland Group's compiler. I didn't try the auto-parallelization, but I did compile MPI with PG's C compiler and AMBER 5.0 with PG's f77 compiler. Here are the results I got (times are in seconds) on my dual PPro 200MHz: g77 opt -O6, ewald test: 496 g77 MPI opt -O6, dual proc, ewald test: 332 pgcc full opt, ewald test: 361 pgcc MPI full opt, dual proc, ewald test: 253 So, dual processors with g77 is faster than one with PGF77, but PGF77 with dual processors is definitely the best. Paralogic is going to let me test on their 4 processor platforms- if this code scales well on intels, it'd definitely be a much cheaper way to get the performance we need. Dave ----------------------------------------------------------------------------- Email: dek@cgl.ucsf.edu David Konerding WWW: http://picasso.ucsf.edu/~dek ----------------------------------------------------------------------------- From yubofan@guomai.sh.cn Tue Jun 9 11:41:29 1998 Received: from guomai.sh.cn ([202.96.206.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA02945 Tue, 9 Jun 1998 11:41:26 -0400 (EDT) Received: from guomai.sh.cn (email-37 [210.0.0.37]) by guomai.sh.cn (8.8.8/8.8.8) with ESMTP id XAA02597 for ; Tue, 9 Jun 1998 23:38:49 +0900 (CDT) Message-ID: <357D57AF.B44EB9E1@guomai.sh.cn> Date: Tue, 09 Jun 1998 23:41:35 +0800 From: Yubo Fan Reply-To: yubofan@guomai.sh.cn X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Partial Optimization Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone: I am doing the geometry optimization of some rather big molecules. Can I split these molecules into some small pieces and optimize them seperately? For example, methyl(4-nitrophenyl)octadecylamine (C18H37N(CH3)C4H4NO2, MNPOA), I want to optimize the geometry of ethylmethyl(4-nitrophenyl)amine (EMNPA) by B3LYP/6-31G*, then change ethyl into octadecyl. Are there some methods in G94W to fix all bond lengths, bond angles and dihedral angles in EMNPA but the ethyl, and change the ethyl into octadecyl? Then do the geometry optimization of NMPOA by PM3 or other semi-empirical methods. With best regards Yubo Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From goddette@tripos.com Thu Jun 11 15:23:09 1998 Received: from gatekeeper.tripos.com (gatekeeper.tripos.com [38.154.18.254]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA19625 Thu, 11 Jun 1998 15:23:08 -0400 (EDT) Received: (from uucp@localhost) by gatekeeper.tripos.com (SMI-8.6/8.6.12) id OAA24490 for <@firewall.tripos.com:chemistry@www.ccl.net>; Thu, 11 Jun 1998 14:20:20 -0500 Received: from elara.tripos.com(192.160.145.60) by gatekeeper.tripos.com via smap (4.0a) id xma024486; Thu, 11 Jun 98 14:20:03 -0500 Received: from centaurus.tripos.com by elara via ESMTP (951211.SGI.8.6.12.PATCH1502/951211.SGI.AUTO) for id OAA03634; Thu, 11 Jun 1998 14:21:24 -0500 Message-ID: <35802ECA.F2AF6928@tripos.com> Date: Thu, 11 Jun 1998 14:23:54 -0500 From: Dean Goddette Reply-To: goddette@tripos.com Organization: Tripos, Inc. X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: 98.07.13 Midwest Molecular Modeling Meeting X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Midwest Molecular Modeling Meeting (M4) APPLICATIONS IN COMPUTER-AIDED DRUG DESIGN July 14, 1998 Indianapolis, Indiana It is my pleasure to announce a Midwest Molecular Modeling Meeting entitled "Applications in Computer-Aided Drug Design", a one-day scientific symposium hosted by Tripos, Inc. to be held on July 14, 1998 in Indianapolis, Indiana. The theme for the meeting is the application of computational chemistry in pharmaceutical/agrochemical research. Topics will include QSAR, combinatorial chemistry and diversity among others. The meeting will take place at the Hyatt Regency, downtown Indianapolis. Registration will begin at 8AM along with breakfast. Talks will begin at 9AM, ending at 3PM with a break for lunch. Registration for the meeting is $80 commercial, $40 academic. For more information or registration information, please see our web site at or contact Jamie Heritage at 1-800-323-2960. -- Dean Goddette, Ph.D. email: goddette@tripos.com Central US & Canada phone: 314-647-1099 x3386 Tripos, Inc. fax: 314-647-9241 1699 South Hanley Road WWW: http://www.tripos.com St. Louis, MO 63144 USA