From chemistry-request@server.ccl.net Thu Dec 30 06:26:24 1999 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA08822 for ; Thu, 30 Dec 1999 06:26:24 -0500 Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.8.7/8.8.7) with ESMTP id NAA01967; Thu, 30 Dec 1999 13:26:13 +0300 Sender: val@nmr-v.ioc.ac.ru Message-ID: <386B3344.DCD2B488@cacr.ioc.ac.ru> Date: Thu, 30 Dec 1999 13:26:12 +0300 From: val Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.35 i586) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net CC: ASG Subject: Re: CCL:high-quality GAMESS-US basis set for iodine? References: <386AB619.C2418252@monmouth.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL-members! Dear Tony! > Having reviewed past CCL messages on the subject, I'm aware of the fact > that the question has been asked before--but no good answer to be > found... Is it possible that there are none available? It seems there is no way to solve the iodine problem in one simple and clear step, at least now. Concerning bases sets, there are some others besides listed in EMSL. In "Chem.Phys.Lett. 1995, 233, p.249" small (I)n molecules were studied and the authors suggested new basis set for iodine. Slightly corrected version of iodine basis set has been used in "Chem.Phys.Lett. 1993, 202, p.495" to study IHI(-) molecule. The 6-311G iodine basis set Tony was asking for, with supplementary diffuse and polarization functions, has been published already, take a look at "J.Chem.Phys. 1995, 103, p.1878". A calibration study on HI and I2 molecules has shown that basis set with g-functions (25s20p14d4f3g) may be required to get reliable results. "Mol.Phys. 1996, 88, p.1645". Even "the simple" I2 molecule may require special attention, see: "J.Chem.Phys. 1997, 107, p.9046", "J.Phys.Chem. A 1997, 101, p.2192". > What do the professionals use to get good geometries and energies of > iodine compounds, even as simple as HI? How much better can MIDI! be > than 3-21G* in this situation? Is my aversion to ECP justified? I > appreciate any comments. The studies cited above probably indicate that one may forget about 3-21G or MIDI if one needs something more than rough estimation. For difficult cases, like [ICl2]-, one may think on developing a new one ;-) ECP is not an absolute must, but the cheapest way to take relativistic effect into account, which can not be neglected for the heaviest of the halogens. Moreover, most of the authors suggest CCSD(T) as electron correlation theory level, which to the best of my knowledge is not implemented in GAMESS-US yet. However, you could try MP4 in PC-GAMESS version of GAMESS-US instead. Happy Y2K! best regards, Valentin. ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Thu Dec 30 07:35:54 1999 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.64.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA10001 for ; Thu, 30 Dec 1999 07:35:53 -0500 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 26680 invoked from network); 30 Dec 1999 11:28:46 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 30 Dec 1999 11:28:46 -0000 Received: (qmail 11233 invoked by uid 10283); 30 Dec 1999 11:28:45 -0000 Message-ID: <19991230112845.11232.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: Re: CCL:high-quality GAMESS-US basis set for iodine? To: val@cacr.ioc.ac.ru (val) Date: Thu, 30 Dec 1999 12:28:45 +0100 (MET) Cc: chemistry@ccl.net In-Reply-To: <386B3344.DCD2B488@cacr.ioc.ac.ru> from "val" at Dec 30, 99 01:26:12 pm X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Unfortunately, it is not true that ECP account for the "relativistic effects" in the Iodine molecule: I guess that spin-orbit effects are more important than scalar-relativistic effects in this case. The ECSs implemented e.g. in Gaussian stick to the nonrelativistic symmetry and do not incorporate spin-orbit effects. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Thu Dec 30 09:16:25 1999 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA10452 for ; Thu, 30 Dec 1999 09:16:25 -0500 Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.8.7/8.8.7) with ESMTP id QAA02388; Thu, 30 Dec 1999 16:15:57 +0300 Sender: val@nmr-v.ioc.ac.ru Message-ID: <386B5B0C.90C4197B@cacr.ioc.ac.ru> Date: Thu, 30 Dec 1999 16:15:56 +0300 From: val Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.35 i586) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net CC: Christoph.van.Wuellen@ruhr-uni-bochum.de Subject: Re: CCL:high-quality GAMESS-US basis set for iodine? References: <19991230112845.11232.qmail@sgi249.rz.ruhr-uni-bochum.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Unfortunately, it is not true that ECP account for the "relativistic > effects" in the Iodine molecule: > I guess that spin-orbit effects are more important than scalar-relativistic > effects in this case. > The ECSs implemented e.g. in Gaussian stick to the nonrelativistic > symmetry and do not incorporate spin-orbit effects. Good! Spin-orbit effect seems to be very important for calculation of various properties, e.g. NMR, etc. Is the same applicable (and really important) for geometry optimization as well? In most cases using ECP usually gives better agreement in geometry compared to all-electron calculations for iodine containing molecules. For example, one may take a look at recent publications with Stuttgart ECP basis set on iodine. Does anybody know appropriate references on what effect: scalar- relativistic or spin-orbit has more effect on geometry? best regards, Valentin. PS. Does "the Iodine molecule" mean I2 only or all iodine containing species? ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Thu Dec 30 09:53:36 1999 Received: from aragorn.ics.muni.cz (aragorn.ics.muni.cz [147.251.4.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA10653 for ; Thu, 30 Dec 1999 09:53:36 -0500 Received: from bilbo.chemi.muni.cz (bilbo.chemi.muni.cz [147.251.28.2]) by aragorn.ics.muni.cz (8.8.5/8.8.5) with ESMTP id OAA02425 for ; Thu, 30 Dec 1999 14:46:26 +0100 (MET) Received: (from czernek@localhost) by bilbo.chemi.muni.cz (8.8.5/8.8.5) id OAA29781; Thu, 30 Dec 1999 14:47:56 +0100 (MET) From: Jiri Czernek Message-Id: <199912301347.OAA29781@bilbo.chemi.muni.cz> Subject: NMR tensors in GAUSSIAN To: chemistry@ccl.net Date: Thu, 30 Dec 1999 14:47:56 +0100 (MET) Cc: czernek@bilbo.chemi.muni.cz (Jiri Czernek) X-Mailer: ELM [version 2.4ME+ PL32 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL-ers , In GAUSSIAN I use IOP33(10=1) to get eigenvalues and eigenvectors of nuclear magnetic shielding tensors. Unfortunatelly, when I run Gaussian 98: SGI64-G98RevA.7 with this IOp to get MP2-GIAO shielding tensors, only eigenvalues and -vectors of SCF tensors are given in the output. I ask you to inform me how to obtain eigenvalues and -vectors of MP2 tensors in g98 as simply as possible. Can somebody help before Y2K? :-) I'll summarize the answers, of course. Cordially , czernek@chemi.muni.cz From chemistry-request@server.ccl.net Thu Dec 30 11:21:56 1999 Received: from zikzak.beaverton.oxmol.com (zikzak.beaverton.oxmol.com [134.172.32.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA11105 for ; Thu, 30 Dec 1999 11:21:56 -0500 Received: from sulfur (dhcp13.baltimore.oxmol.com [134.172.65.13]) by zikzak.beaverton.oxmol.com (8.9.1/8.9.1) with ESMTP id HAA24029; Thu, 30 Dec 1999 07:14:40 -0800 Message-Id: <4.2.0.58.19991230101117.00a533c0@zikzak.beaverton.oxmol.com> Date: Thu, 30 Dec 1999 10:16:49 -0500 To: rsusnow@physiome.com From: Doug Smith Subject: toxicity prediction Cc: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Roberta: >Date: Tue, 28 Dec 1999 13:37:12 -0500 > >Hi, > > I would like to find out what software is available for the prediction of >metabolites from a parent compound. I am also interested in the associated >toxicology prediction. Please send the response directly to me and I will post them >on the list. Thank you. TOPKAT is a toxicity prediction program developed at Health Designs, Inc., now a part of Oxford Molecular Group. TOPKAT uses Kier & Hall electrotopological states (E-states) as well as shape, symmetry, MW, and logP as descriptors to build statistically robust Quantitative Structure Toxicity Relationship (QSTR) models for over 18 endpoints. Another five models and endpoints are currently in development. TOPKAT runs on PCs under Windows 95/98/NT, and the new version, 6.0, will be released around April 1, 2000. TOPKAT will validate its assessments via a univariate analysis of the descriptors, a patented multivariate analysis of the fit of the query structure in Optimum Prediction Space, and by similarity searching in descriptor space. If you would like additional information on the program, toxic endpoints calculated, or prices, please email me directly. Sincerely, Doug Smith Dr. Douglas A. Smith, Ph.D. tel. 410-527-4500 Business Development Manager fax 410-527-4599 Toxicology Products and Services email dsmith@oxmol.com Oxford Molecular Group web www.oxmol.com 11350 McCormick Road Executive Plaza III Suite 1100 Hunt Valley, MD 21031 From chemistry-request@server.ccl.net Thu Dec 30 19:49:05 1999 Received: from pop.telekabel.at (pop.telekabel.at [195.34.134.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA13031 for ; Thu, 30 Dec 1999 19:49:04 -0500 Received: from mgate3.telekabel.at ([195.34.133.22]) by pop.telekabel.at (Post.Office MTA v3.5.2 release 221 ID# 0-63669U50000L50000S0V35) with ESMTP id at; Thu, 30 Dec 1999 00:35:45 +0100 Received: from vienna.at ([212.186.101.105]) by mgate3.telekabel.at (Post.Office MTA v3.5.3 release 223 ID# 0-57067U15000L15000S0V35) with ESMTP id at; Thu, 30 Dec 1999 00:35:27 +0100 Message-ID: <386A9A9F.8574EC56@vienna.at> Date: Thu, 30 Dec 1999 00:34:55 +0100 From: Gerald Loeffler Organization: Daemonstration Software Consulting X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en,de MIME-Version: 1.0 To: Christoph.van.Wuellen@ruhr-uni-bochum.de CC: chemistry@ccl.net Subject: Re: CCL:What exactly is LINDA References: <19991229093143.27260.qmail@sgi249.rz.ruhr-uni-bochum.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! Linda is an implementation of the (by now almost classical) concept of tuple-space, which is quite similar to a message-board that is shared by otherwise completely independent processes. These processes can leave messages (data) at the message-board and collect messages (data) from the message-board. The tuple-space is thus a communication mechanism for distributed and/or parallel computing. In principle you should be able to implement a tuple-space on top of different inter-process communication mechanisms like sockets, MPI, etc. I don't know what Linda itself uses - but it really doesn't matter because you are shielded from this. Hoping that I'm not being unfair, I'd say that any concept (like that of a shared message-board) that uses a single, shared resource doesn't scale well with the number of processes trying to access this shared resource. Hence I'd guess that you get a very intuitive programming model at the expense of limited scalability. This whole idea quite recently came to new fame with a Java implementation (Jini / JavaSpaces). cheers, gerald Christoph.van.Wuellen@ruhr-uni-bochum.de wrote: > > What (exactly) is LINDA? Is it (merely) a message-passing library > a la PVM or MPI with a user-interface simulating a virtual shared > memory? What are you really paying for if you buy LINDA? > > LINDA is known to me only in the context of parallel GAUSSIAN, so what > is the advantage of LINDA over PVM or MPI or other portable and > more-or-less standardized message passing systems? -- Does the combination > GAUSSIN/LINDA beat alternative implementations (e.g. with PVM) in terms > of speed or ease-of-use? > > ---------------------------+------------------------------------------------ > Christoph van Wullen | Fon (University): +49 234 32 26485 > Theoretical Chemistry | Fax (University): +49 234 32 14109 > Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 > D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de > ---------------------------+------------------------------------------------ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Gerald Loeffler - Daemonstration Software Consulting WWW: http://www.daemonstration.com Email: Gerald.Loeffler@vienna.at Phone: +43 676 3289588 Fax: +43 676 3509846 Smail: Siebensterngasse 46/4/114, A-1070 Vienna, Austria Keywords: OOA&D, Java, J2EE, EJB, ODBMS, RDBMS, XML, Corba, RMI, DNA Chip Technology, Computational Biology From chemistry-request@server.ccl.net Thu Dec 30 21:19:02 1999 Received: from thalia.fm.intel.com (thalia.fm.intel.com [132.233.247.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA13471 for ; Thu, 30 Dec 1999 21:19:02 -0500 Received: from SMTP (fmsmsxvs02-1.fm.intel.com [132.233.42.202]) by thalia.fm.intel.com (8.9.1a+p1/8.9.1/d: relay.m4,v 1.13 1999/12/30 20:05:58 dmccart Exp $) with SMTP id VAA29497 for ; Thu, 30 Dec 1999 21:11:43 GMT Received: from fmsmsx18.intel.com ([132.233.48.18]) by 132.233.48.202 (Norton AntiVirus for Internet Email Gateways 1.0) ; Fri, 31 Dec 1999 01:11:44 0000 (GMT) Received: by fmsmsx18.fm.intel.com with Internet Mail Service (5.5.2448.0) id ; Thu, 30 Dec 1999 17:11:43 -0800 Message-ID: From: "Mattson, Timothy G" To: chemistry@ccl.net Subject: RE: What exactly is LINDA Date: Thu, 30 Dec 1999 17:11:42 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" This is getting a bit off the topic of computational chemistry, so I will try and keep it short. In Gerald's last post, he questioned the scalability of Linda. This is a common misconception, so I just couldn't let it slip by. The Linda implementation from Scientific Computing Associates (which is the one used with Gaussian) scales very well with the number of nodes. It uses a compile time analysis that translates operations on a tuple space into efficient message passing operations. I have seen Linda jobs run on 128 nodes and there is no reason it can't go further (and actually, it probablly has --- I just don't recall seeing it done). The Computer science literature describes in detail how the Linda compiler pulls off this trick. I gave a reference to one paper in a previous post that deals with this. There is another paper that directly compares the performance of Linda to message passing systems. The reference to this paper is: "The Linda alternative to message-passing systems" Parallel Computing, vol 20, pp. 633-655, 1994. Nicholas J. Carriero, David Gelernter, Timothy G. Mattson, and Andrew H. Sherman I won't bore the members of this list with the details, but if anyone wants to talk to me about this further, feel free to send email. --Tim > -----Original Message----- > From: Gerald Loeffler [SMTP:Gerald.Loeffler@vienna.at] > Sent: Wednesday, December 29, 1999 3:35 PM > To: Christoph.van.Wuellen@ruhr-uni-bochum.de > Cc: chemistry@ccl.net > Subject: CCL:What exactly is LINDA > > Hi! > > Linda is an implementation of the (by now almost classical) concept of > tuple-space, which is quite similar to a message-board that is shared by > otherwise completely independent processes. These processes can leave > messages (data) at the message-board and collect messages (data) from > the message-board. The tuple-space is thus a communication mechanism for > distributed and/or parallel computing. > > In principle you should be able to implement a tuple-space on top of > different inter-process communication mechanisms like sockets, MPI, etc. > I don't know what Linda itself uses - but it really doesn't matter > because you are shielded from this. > > Hoping that I'm not being unfair, I'd say that any concept (like that of > a shared message-board) that uses a single, shared resource doesn't > scale well with the number of processes trying to access this shared > resource. Hence I'd guess that you get a very intuitive programming > model at the expense of limited scalability. > > This whole idea quite recently came to new fame with a Java > implementation (Jini / JavaSpaces). > > cheers, > gerald > > Christoph.van.Wuellen@ruhr-uni-bochum.de wrote: > > > > What (exactly) is LINDA? Is it (merely) a message-passing library > > a la PVM or MPI with a user-interface simulating a virtual shared > > memory? What are you really paying for if you buy LINDA? > > > > LINDA is known to me only in the context of parallel GAUSSIAN, so what > > is the advantage of LINDA over PVM or MPI or other portable and > > more-or-less standardized message passing systems? -- Does the > combination > > GAUSSIN/LINDA beat alternative implementations (e.g. with PVM) in terms > > of speed or ease-of-use? > > > > > ---------------------------+---------------------------------------------- > -- > > Christoph van Wullen | Fon (University): +49 234 32 26485 > > Theoretical Chemistry | Fax (University): +49 234 32 14109 > > Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 > > D-44780 Bochum, Germany | eMail: > Christoph.van.Wuellen@Ruhr-Uni-Bochum.de > > > ---------------------------+---------------------------------------------- > -- > > > > -- > Gerald Loeffler - Daemonstration Software Consulting > WWW: http://www.daemonstration.com > Email: Gerald.Loeffler@vienna.at > Phone: +43 676 3289588 > Fax: +43 676 3509846 > Smail: Siebensterngasse 46/4/114, A-1070 Vienna, Austria > Keywords: OOA&D, Java, J2EE, EJB, ODBMS, RDBMS, XML, Corba, RMI, > DNA Chip Technology, Computational Biology > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > >