From chemistry-request@server.ccl.net Mon Feb 10 07:24:16 2003 Received: from tri-e2k.d.ethz.ch ([129.132.112.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1ACOGI17303 for ; Mon, 10 Feb 2003 07:24:16 -0500 Received: from xfe2.d.ethz.ch ([192.168.36.11]) by tri-e2k.d.ethz.ch with Microsoft SMTPSVC(5.0.2195.5329); Mon, 10 Feb 2003 13:24:16 +0100 Received: from tech.chem.ethz.ch ([129.132.224.193]) by xfe2.d.ethz.ch with Microsoft SMTPSVC(5.0.2195.5329); Mon, 10 Feb 2003 13:24:15 +0100 Message-ID: <3E479A5D.B394D3D0@tech.chem.ethz.ch> Date: Mon, 10 Feb 2003 13:26:05 +0100 From: angelo vargas Organization: ETHZ X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re:Gaussian 98 Molecular Mechanics input References: <002501c2cdd0$f5d0f900$2f7935a1@pharma.hr> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-OriginalArrivalTime: 10 Feb 2003 12:24:15.0704 (UTC) FILETIME=[5390ED80:01C2D0FF] Hallo Can anyone send me an imput for a Gaussian 98 AMBER calculation? Is it possible to make a constrained optimization with G98 Molecular Mechanics? Angelo Vargas _______________________________________________________________________ Angelo Vargas Laboratory of Technical Chemistry Department of Chemical Engineering and Industrial Chemistry Swiss Federal Institute of Technology (ETHZ) ETH Hönggerberg, Telefon: 0041/1/633 42 32, Room HCl E 129 Zürich - Switzerland Fax: 0041/1/632 11 63 E-mail: vargas@tech.chem.ethz.ch http://mercury.ethz.ch/members/vargas/ ________________________________________________________________________ From chemistry-request@server.ccl.net Mon Feb 10 05:45:36 2003 Received: from tri-e2k.d.ethz.ch ([129.132.112.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1AAjZI14750 for ; Mon, 10 Feb 2003 05:45:36 -0500 Received: from xfe2.d.ethz.ch ([192.168.36.11]) by tri-e2k.d.ethz.ch with Microsoft SMTPSVC(5.0.2195.5329); Mon, 10 Feb 2003 11:45:35 +0100 Received: from tech.chem.ethz.ch ([129.132.224.193]) by xfe2.d.ethz.ch with Microsoft SMTPSVC(5.0.2195.5329); Mon, 10 Feb 2003 11:45:35 +0100 Message-ID: <3E47833D.24799D8D@tech.chem.ethz.ch> Date: Mon, 10 Feb 2003 11:47:25 +0100 From: angelo vargas Organization: ETHZ X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: References: <200111121748.fACHmH92634844@mail.rochester.edu> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-OriginalArrivalTime: 10 Feb 2003 10:45:35.0012 (UTC) FILETIME=[8A8F0640:01C2D0F1] Hello all can anybody send me an example of a G98 input file for an AMBER molecular mechanics calculation? Can you do a constrained calculation with G98 molecular mechanics? The guide is extremely synthetic concerning this module. Thanks Angelo _______________________________________________________________________ Angelo Vargas Laboratory of Technical Chemistry Department of Chemical Engineering and Industrial Chemistry Swiss Federal Institute of Technology (ETHZ) ETH Hönggerberg, Telefon: 0041/1/633 42 32, Room HCl E 129 Zürich - Switzerland Fax: 0041/1/632 11 63 E-mail: vargas@tech.chem.ethz.ch http://mercury.ethz.ch/members/vargas/ ________________________________________________________________________ From chemistry-request@server.ccl.net Mon Feb 10 07:16:56 2003 Received: from alpha.cerm.unifi.it ([150.217.146.11]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h1ACGuI16956 for ; Mon, 10 Feb 2003 07:16:56 -0500 Received: (qmail 15460 invoked by uid 204); 10 Feb 2003 11:53:27 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 10 Feb 2003 11:53:26 -0000 Date: Mon, 10 Feb 2003 12:53:26 +0100 (CET) From: Robert Sbaglia To: Subject: SMILES Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS perl-11 Hi, Was wondering if anyone had any tips for converting from SMILE format to mol or mol2 format? Thanks, Rob Sbaglia CERM University of Florence From chemistry-request@server.ccl.net Mon Feb 10 06:11:57 2003 Received: from venus.phpwebhosting.com ([64.29.16.27]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h1ABBuI15635 for ; Mon, 10 Feb 2003 06:11:56 -0500 Received: (qmail 3163 invoked from network); 10 Feb 2003 11:11:56 -0000 Received: from unknown (HELO localhost.leitl.org) (217.80.40.2) by venus.phpwebhosting.com with SMTP; 10 Feb 2003 11:11:56 -0000 Received: from localhost (eugen@localhost) by localhost.leitl.org (8.11.6/8.11.6) with ESMTP id h1ABBmf16748 for ; Mon, 10 Feb 2003 12:11:51 +0100 X-Authentication-Warning: localhost.localdomain: eugen owned process doing -bs Date: Mon, 10 Feb 2003 12:11:48 +0100 (CET) From: Eugen Leitl X-X-Sender: To: Subject: Poor scaling (was Re: Question about custers) (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Mon, 10 Feb 2003 11:47:38 +0100 (CET) From: Bogdan Costescu To: Ken Chase Cc: Beowulf List Subject: Poor scaling (was Re: Question about custers) On Fri, 7 Feb 2003, Ken Chase wrote: > Im curious, when people see really poor scaling on their clusters (HSI > or GBE or 100BT, doesnt matter) at like 16 or 32 or more nodes (Im thinking > CHARMM and Gromacs here), what do you do with the extra cpu? Well, this is for the case when you have SMP nodes and run only one process per node. I agree that this scales better, but for administrative reasons this is not always the case... Based on a similar reasoning and Moore's law, we never bought a one-time large number of nodes for running CHARMM. Instead, we always buy multiple of 4 in the range 4-16, sometimes UP, sometimes SMP (the multiple of 4 thing is not because it's a power of 2 or somehow related to CHARMM but because it's the number of computer cases that fit on one of our shelves :-)). Because they are often of different speeds and sometimes connected to different switches, it's really not efficient to run on nodes bought in different batches, so we limit in this way the maximum number of CPUs that can be allocated to a job. > Just let it float away unused? Do you use it? Do you run other jobs on > them at the same time? We usually use the SMP nodes in 2 ways: - 2 jobs: one parallel and one single. As CHARMM still has important features that do not run in parallel (f.e. normal modes), we run one of these (usually large memory-) jobs along with a (usually low memory-) parallel one. This requires SMP nodes with large amounts of memory (>=1Gb) - 2 parallel jobs. We have found (by trying, so don't get this as the definitive answer!) that the total throughput is higher; this however is true only when the jobs have similar data sizes - if the jobs have numbers of atoms that are one degree or more different, this is not true anymore. > Do you nice those jobs to 19? No, we usually let them run at normal priority. At least in the first case they don't seem to interfere with each other. In the second case, we know that there will be interference (even in the case of HSI - Myrinet here), so we just say "That's life" :-) > Do you see your cache being thrashed by this How do you quantify the cache thrashes ? I've found that CHARMM scales surprisingly well with CPU speed for classical MD jobs and not affected much by cache size; this comes only > from job-level timing, for various reasons I've never been able to include some CPU counter library in the "production" cluster kernels. Until now (P4-Xeon era) I haven't seen a significant speed improvement when compiled with PGI compilers vs. fort77+f2c+gcc2.x (which for me always generated faster code than g77 -O6 and all other optimizations present in the CHARMM Makefile). I didn't have time yet to test how the speed compares on Xeons with f2c+gcc-2.x vs. g77-3.x vs. PGI vs. Intel compilers. Why I'm saying this: because I believe that the speed gain from gcc-3.x/PGI/Intel compilers would come from better memory access patterns which would more fully use the cache and so the effect of cache thrashing would be more evident - please correct me if I'm talking rubbish. -- Bogdan Costescu IWR - Interdisziplinaeres Zentrum fuer Wissenschaftliches Rechnen Universitaet Heidelberg, INF 368, D-69120 Heidelberg, GERMANY Telephone: +49 6221 54 8869, Telefax: +49 6221 54 8868 E-mail: Bogdan.Costescu@IWR.Uni-Heidelberg.De _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf From chemistry-request@server.ccl.net Mon Feb 10 09:18:11 2003 Received: from helix.nih.gov ([128.231.2.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1AEIAI20273 for ; Mon, 10 Feb 2003 09:18:10 -0500 Received: (from mn1@localhost) by helix.nih.gov (8.11.6/8.11.6) id h1AEI1o1219268; Mon, 10 Feb 2003 09:18:01 -0500 (EST) Date: Mon, 10 Feb 2003 09:18:01 -0500 From: "M. Nicklaus" To: Robert Sbaglia cc: chemistry@ccl.net Subject: Re: CCL:SMILES In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 10 Feb 2003, Robert Sbaglia wrote: > Was wondering if anyone had any tips for converting from SMILE format to > mol or mol2 format? Check out our Online SMILES Translator service at http://cactus.nci.nih.gov/services/translate/ Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design MiniCore Facility Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Feb 10 09:00:43 2003 Received: from camdmail01.cam.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1AE0hI19820; Mon, 10 Feb 2003 09:00:43 -0500 To: Robert Sbaglia Cc: chemistry@ccl.net, "Computational Chemistry List" Subject: Re: CCL:SMILES MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: rcompton@accelrys.com Date: Mon, 10 Feb 2003 14:00:40 +0000 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 02/10/2003 02:00:43 PM, Serialize complete at 02/10/2003 02:00:43 PM 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 h1AE0hI19821 You can use the Accelrys DS ViewerLite to import & export the following formats. http://www.accelrys.com/dstudio/ds_viewer/viewerlite [For systematic use, I'd take a look at the Accord SDK. http://www.accelrys.com/accord/sdk.html] Import: Viewer (msv; binary, Microsoft compound document) Brookhaven PDB (pdb, ent) MDL MOL (mol, sdf, sd, mdl) Insight CAR (car) Quanta (msf) Cerius2 (msi) Catalyst (cpd, chm) InsightII Grid (grd) Cambridge Crystallographic (csd, fdat, dat) Sybyl MOL2 (mol2) Crystallographic Information (cif) XYZ Coordinate (XYZ) Smiles (smi) MDL Sketch (skc) Export: Viewer (msv) Brookhaven PDB (pdb, ent) MDL MOL (mol, sdf, sd, mdl) XYZ Coordinate (XYZ) Catalyst (cpd, chm) VRML World (wrl) POV-Ray Scene (pov) Smiles (smi) Image (gif, jpg, bmp) Kind regards, Richard. _________________________________________ Mr Richard Compton Regional Director Accelrys Ltd. 334 Cambridge Science Park Cambridge CB4 0WN Office Tel. +44 1223 228 500 Office Fax. +44 1223 228 501 Direct Tel. +44 1223 228 546 Mobile +44 7740 029 611 Web. http://www.accelrys.com Email. rcompton@accelrys.com We're looking forward to seeing you at AccelrysWorld 2003 in San Diego, February 24 - 26. Confirmed speakers include: Professor Dr. Robert Huber, Director, Max-Planck-Institut für Biochemie Professor Sir Harry Kroto FRS, Professor of Chemistry, University of Sussex Dr. Richard Blint, General Motors Dr. Leroy Hood, Director & President, Institute for Systems Biology Dr. Christopher Lipinski, Adjunct Research Fellow, Pfizer Dr. William Pulleyblank, Director Deep Computing Institute, IBM http://www.accelrys.com/accelrysworld/abstract_bios.html Cerius2 4.8 Now available with three new modules C2.LibX - Design better focused libraries from extremely large virtual pools C2.NNet - Apply the power of Back Propagation Neural Networks to your SAR problems C2.AutoLudi - Extend C2.Ludi's de novo engine to design better lead candidates against a target structure Robert Sbaglia Sent by: "Computational Chemistry List" 10/02/2003 11:53 To: cc: Subject: CCL:SMILES Hi, Was wondering if anyone had any tips for converting from SMILE format to mol or mol2 format? Thanks, Rob Sbaglia CERM University of Florence -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon Feb 10 11:15:43 2003 Received: from crane2.cf.ac.uk ([131.251.0.25]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1AGFgI23691 for ; Mon, 10 Feb 2003 11:15:43 -0500 Received: from thor.cf.ac.uk ([131.251.0.1]) by crane2.cf.ac.uk with esmtp (Exim 4.05) id 18iGap-0005Vd-00; Mon, 10 Feb 2003 16:15:39 +0000 Received: from localhost (sacjap@localhost) by thor.cf.ac.uk (8.8.8/8.6.12) with ESMTP id QAA01067; Mon, 10 Feb 2003 16:15:38 GMT Date: Mon, 10 Feb 2003 16:15:38 +0000 (GMT) From: Jamie Platts X-Sender: sacjap@thor To: Robert Sbaglia cc: chemistry@ccl.net Subject: Re: CCL:SMILES In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Robert - we've found that Gasteiger's CORINA program works well, generating good 3D structures from SMILES strings and outputting in mol/SD format. Take a look at http://www2.chemie.uni-erlangen.de/software/corina/index.html Cheers, Jamie > > Hi, > > Was wondering if anyone had any tips for converting from SMILE format to > mol or mol2 format? > > Thanks, > > Rob Sbaglia > CERM > University of Florence > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Mon Feb 10 10:46:42 2003 Received: from mailshell.com ([209.157.66.231]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h1AFkgI22871 for ; Mon, 10 Feb 2003 10:46:42 -0500 Received: (qmail 31276 invoked by uid 99); 10 Feb 2003 15:46:40 -0000 Message-ID: <1044892000.3e47c96083d73@www.mailshell.com> Date: Mon, 10 Feb 2003 07:46:40 -0800 X-Priority: 3 (Normal) From: To: chemistry@ccl.net Subject: SUMMARY Re: CCL:external basis sets in GAMESS In-Reply-To: <001a01c2cdaa$04ca5ae0$0201a8c0@hppav> MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 8bit User-Agent: Mailshell.com Firts, thanks to all the people who helped me with this problem! It turned out that my final stumbling block in the way of defining the external basis sets was the sometimes unexpected pickiness of GAMESS for formatting its $DATA input (exacerbated by the cryptic nature of some error messages). Specifically, there MUST be a blank line before the closing $END, after the last line of basis set definitions! Other important things to keep in mind: you cannot specify external basis set in $data with coord = CART, ZMT, or ZMTMPC. Use coord=UNIQUE instead! Also, there seems to be no way in pcGAMESS to read basis sets from an external file (defined by EXTBAS, as per the latest GAMESS-US manual): the program doesn't recognize the required EXTFIL flag as a valid keyword in $BASIS! In other words, pasting into $DATA should be applied instead (even though the error message upon trying other than coord=UNIQUE tells "SPECIFY THE BASIS SET WITH $BASIS")... In any event, the most useful part of the error messages DID apply, i.e.: WE LEARN MORE FROM LOSING THAN WE DO FROM WINNING. Thanks to the example input supplied by Jim Kress I found out that it is possible to run MP4 in pcGAMESS (despite what its doc says). This of course brings up the question whether anyone knows of a more up-to-date description of what pcGAMESS can actually do - apparently, its somewhere between what its own manual says and what the GAMESS-US docs describe ;- Jim Kress Alex. A. Granovsky -- Zoli Fekete _______________________________________________________ The FREE service that prevents junk email http://www.mailshell.com From chemistry-request@server.ccl.net Mon Feb 10 13:49:04 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1AIn4I29115 for ; Mon, 10 Feb 2003 13:49:04 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h1AIn4j27773 for ; Mon, 10 Feb 2003 13:49:04 -0500 (EST) Date: Mon, 10 Feb 2003 13:49:02 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: 03.04.07 Modeling & Simulation Summer School- Toulouse, France Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT Dear colleagues, we are pleased to announce the PSSIT-2003 organized by LPST/IRSAMC-LAAS-ATOMCAD : -- PHYSICS SPRING SCHOOL IN TOULOUSE (PSSIT 2003) -- Modeling and Simulation in Micro and Nano Technologies and Materials Engineering Toulouse - FRANCE, April 7th - 11th, 2003 http://www.lpst.ups-tlse.fr/PSSIT cordially, Georges -- Georges Landa Laboratoire de Physique des Solides de Toulouse (LPST) UMR 5477 - CNRS - IRSAMC - Université Paul Sabatier 31062 Toulouse cedex 4 (France) mél : Georges.Landa@lpst.ups-tlse.fr Tel : 33 (0) 561 556 549 Fax : 33 (0) 561 556 233 Laboratoire : http://www.lpst.ups-tlse.fr Institut : http://www.irsamc.ups-tlse.fr SFP : http://www.lpst.ups-tlse.fr/SFP PSSIT-2003 : http://www.lpst.ups-tlse.fr/PSSIT From chemistry-request@server.ccl.net Mon Feb 10 09:51:06 2003 Received: from mail.zrz.tu-berlin.de ([130.149.4.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1AEp6I21156 for ; Mon, 10 Feb 2003 09:51:06 -0500 Received: from mail.zrz.tu-berlin.de ([130.149.4.15]) by mail.zrz.tu-berlin.de with esmtp (exim-3.36) for id 18iFGz-0000wO-00; Mon, 10 Feb 2003 15:51:05 +0100 Received: from mail.zrz.TU-Berlin.DE ([130.149.4.15]) by mail.zrz.TU-Berlin.DE (MailMonitor for SMTP v1.2.0 ) ; Mon, 10 Feb 2003 15:51:05 +0100 (CET) Received: from mailbox.tu-berlin.de ([130.149.4.18]) by mail.zrz.tu-berlin.de with esmtp (exim-3.36) for id 18iFGz-0000wJ-00; Mon, 10 Feb 2003 15:51:05 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailbox.tu-berlin.de with esmtp (exim-3.36) for id 18iFGz-0003sx-00; Mon, 10 Feb 2003 15:51:05 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailbox.zrz.tu-berlin.de Message-Id: Date: Mon, 10 Feb 2003 15:50:14 +0100 To: chemistry@ccl.net From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: REHE2003 --- Conference on Relativistic Effects Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" X-Virus-Scanned: Sophos MailMonitor on mail.zrz.tu-berlin.de; Mon, 10 Feb 2003 15:51:05 +0100 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h1AEp6I21157 ====================================================================== "RELATIVISTIC EFFECTS IN HEAVY-ELEMENT CHEMISTRY" (satellite meeting to the ICQC 2003 in Bonn) Berlin (Germany), July 28-30, 2003 SECOND CIRCULAR ====================================================================== Dear colleague, as a satellite meeting to the International Congress in Quantum Chemistry (ICQC), there will be a symposium on "RELATIVISTIC EFFECTS IN HEAVY-ELEMENT CHEMISTRY" to be held in Berlin, July 27-30, 2003, at the Technical University. ========================= The date is chosen such that it might be most convenient for those of you who attend the main meeting, the ICQC 2003 in Bonn, July 20-26, 2003. The REHE2003 homepage http://www.chemie.tu-berlin.de/REHE2003 has been updated. You will find information on the scientific programme, the (preliminary) schedule, how to register, how to submit an abstract for a poster / a contributed talk, and information on accomodation for the three days. Please have a look at it, and if there are further questions, do not hesitate to send me an e-mail. Yours, +---------------------------------+----------------------------------+ | Prof. Christoph van Wüllen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universität Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Straße des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+----------------------------------+ From chemistry-request@server.ccl.net Mon Feb 10 15:51:44 2003 Received: from sgofims02.ccs.ppg.com ([141.189.251.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1AKpiI00465 for ; Mon, 10 Feb 2003 15:51:44 -0500 Received: by sgofims02.ccs.ppg.com with Internet Mail Service (5.5.2653.19) id <1WC4ZNMN>; Mon, 10 Feb 2003 15:51:44 -0500 Message-ID: <3251EC702A37B9458A01D917C3D3B389021F4C@sgofusr20.nac.ppg.com> From: "Deng, Jun" To: "'chemistry@ccl.net'" Subject: visualization Date: Mon, 10 Feb 2003 15:51:41 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear all: Will you point out to me how to visualize x, y, z axis, principle moment of inertia, dipole moment and transition dipole moment calculated by Gaussian98? Thank you in advance! Jun Deng From chemistry-request@server.ccl.net Mon Feb 10 19:26:05 2003 Received: from mailrelay2.lanl.gov ([128.165.4.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1B0Q5I04998 for ; Mon, 10 Feb 2003 19:26:05 -0500 Received: from swan.lanl.gov (localhost.localdomain [127.0.0.1]) by mailrelay2.lanl.gov (8.12.3/8.12.3/(ccn-5)) with ESMTP id h1B0Q4gp019006 for ; Mon, 10 Feb 2003 17:26:04 -0700 Received: from heron.lanl.gov (heron.lanl.gov [128.165.96.39]) by swan.lanl.gov (8.12.1/8.12.1) with ESMTP id h1B0L8xS027086 for ; Mon, 10 Feb 2003 17:21:08 -0700 Received: from localhost (tamulis@localhost) by heron.lanl.gov (8.12.1/8.12.1) with ESMTP id h1AHL2aE003779 for ; Mon, 10 Feb 2003 10:21:02 -0700 Date: Mon, 10 Feb 2003 10:21:02 -0700 (MST) From: "Temporary Guest Account;CNLS;7-1444;9999999" To: Subject: Decoherence of spins Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Would you please to give literature reference concerning calculations of decoherence of nucleus and electron spins that disturb molecular NMR and ESR computing. Best regards, Arvydas Tamulis ******************************************************************* Temporal address until 30 April 2003: Los Alamos National Laboratory Center for Nonlinear Studies P.O. Box 1663, Mail Stop B258 Los Alamos, New Mexico 87545 Work Phone: 1 505 667-7278 Fax: 1 505 665-2659 e-mail: tamulis@cnls.lanl.gov ******************************************************************* From chemistry-request@server.ccl.net Mon Feb 10 23:19:54 2003 Received: from marcy.nas.nasa.gov ([129.99.113.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1B4Jsp08285 for ; Mon, 10 Feb 2003 23:19:54 -0500 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.6+Sun/8.11.6/NAS 8.11.6-5n) with ESMTP id h1B4Jm107163 for ; Mon, 10 Feb 2003 20:19:49 -0800 (PST) Date: Mon, 10 Feb 2003 20:19:48 -0800 (PST) From: Ioana Cozmuta To: Computational Chemistry List Subject: references Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Could anyone please point me out to some good papers that discuss the following two issues (or related): 1. what is the best approach to simulate ionic solutions (for example, if in experiments the solution is 1M KCl what is the most accurate way to treat this in simulations: cutoff, etc, any details that one should be aware of) 2. simulations of single stranded DNA or RNA polymers (what are some tipical conformations, how do they depend on the pH of the solution etc). Thank you very much in advance, Ioana ********************************* * Ioana Cozmuta, PhD * * NASA-AMES Research Center * * Mail Stop 230-3 * * Moffet Field,CA 94035 * * phone: (650) 604-0993 * * fax: (650) 604-0350 * *********************************