From chemistry-request@server.ccl.net Tue Mar 28 00:02:36 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id AAA30586 for ; Tue, 28 Mar 2000 00:02:28 -0500 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Tue, 28 Mar 2000 13:05:32 +0800 Sender: user@ccl.net Message-ID: <38E03CAB.17E7410@iris.sipp.ac.cn> Date: Tue, 28 Mar 2000 13:01:31 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: problem in TS searching Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello everyone: I met a strange thing in transition state searching in MOPAC. There are three reactants, HOCH2CH2NH2, H2O and HCONH2 to complete the reaction like the following: NH2 | HOCH2CH2NH2+H2O+HCONH2--->(+)NH3CH2CH2O(-)+ H2O +HCONH2 ---> (+)NH3CH2CH2O-C-O(-) +H2O | H I use pseudo reaction coordinate technique to find the transtion state of the first reaction, but when I use PM3 MMOK TS PRECISE to refine it, I failed. Then I cut off the HCONH2 from the system, I can refine the first TS I got, because I got one negative frequency. Does anyone have some experients about the problem I met, hope you can give me some suggestion. Thank in advance. Regards, mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Mao Xiang | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Tue Mar 28 03:50:18 2000 Received: from gatekeeper.bnfl.co.uk ([193.35.7.249]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA31940 for ; Tue, 28 Mar 2000 03:50:15 -0500 From: scott.l.owens@bnfl.com Received: by gatekeeper.bnfl.co.uk; id JAA12140; Tue, 28 Mar 2000 09:50:20 +0100 (BST) Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper.bnfl.co.uk via smap (3.2) id xma012118; Tue, 28 Mar 00 09:50:10 +0100 Received: from ASN027.bnfl.com (unverified) by ANT008.SPR.BNFL.COM (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Tue, 28 Mar 2000 09:56:10 +0100 Received: from BNotesMTA1.sell.bnfl.com ([10.10.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id JAA08114 for ; Tue, 28 Mar 2000 09:48:40 +0100 (BST) Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.1 (569.2 2-6-1998)) id 002568B0.0035E6B4 ; Tue, 28 Mar 2000 09:48:44 +0000 X-Lotus-FromDomain: BNFL To: CHEMISTRY@ccl.net Message-Id: <002568B0.0034A3FB.00@BNotesMTA1.sell.bnfl.com> Date: Tue, 28 Mar 2000 09:47:59 +0000 Subject: Problems with HOMO/LUMO gap MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Hi there all, a question which has been as issue for some time which I seem to be stuck with is the problem of getting SCF convergence when there is a small HOMO/LUMO gap. The program that we are using is DMol3 by MSI. Specifically the problem relates to structural optimisation of actinide containing molecules - especially those which are not "stable" (e.g. UF4H). There are several procedures which are recommended to get around this including smearing the orbitals (to allow partial occupancy) and level shift (where the vitual orbitals are just moved out of harms way). However neither of these methods seems to improve convergence more than marginally (they may converge once or twice but usually fail as the structure nears an optimum geometry). Has anyone any experience with other systems which do not converge for similar reasons? If so what did you find that solved the problem or helped at all? Thanks - I will summarise for the list if I get any replies. Scott Owens slo1@bnfl.com From chemistry-request@server.ccl.net Tue Mar 28 03:35:20 2000 Received: from gatekeeper.bnfl.co.uk ([193.35.7.249]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA31853 for ; Tue, 28 Mar 2000 03:35:17 -0500 From: scott.l.owens@bnfl.com Received: by gatekeeper.bnfl.co.uk; id JAA09218; Tue, 28 Mar 2000 09:35:20 +0100 (BST) Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper.bnfl.co.uk via smap (3.2) id xma009181; Tue, 28 Mar 00 09:35:10 +0100 Received: from ASN027.bnfl.com (unverified) by ANT008.SPR.BNFL.COM (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Tue, 28 Mar 2000 09:40:59 +0100 Received: from BNotesMTA1.sell.bnfl.com ([10.10.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id JAA07690 for ; Tue, 28 Mar 2000 09:33:29 +0100 (BST) Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.1 (569.2 2-6-1998)) id 002568B0.0034965F ; Tue, 28 Mar 2000 09:34:23 +0000 X-Lotus-FromDomain: BNFL To: CHEMISTRY@ccl.net Message-Id: <002568B0.0033AD86.00@BNotesMTA1.sell.bnfl.com> Date: Tue, 28 Mar 2000 09:34:22 +0000 Subject: MC routines MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Hi there all, I made a request as follows: "I am trying to get hold of source code for performing Monte Carlo simulations on molecular/ionic periodic systems which includes an implementation of Ewald, if anyone has or knows of such a source code (in some flavour of C or FORTRAN) then could you get in touch with me. We need to be able to edit the routines to include some non-standard MC procedures." There were only a few replies - thanks to Rafael R. Pappalardo and Keith Refson for the replies. Two sources - either the code "Monte" by Dr Neal Skipper at University College, London, or the CCP5 archives at ftp://ftp.dl.ac.uk/ccp5/ - haven't had any feedback from colleague who was interested in this so no idea as yet what these source have available. Thanks Scott Owens slo1@bnfl.com From chemistry-request@server.ccl.net Tue Mar 28 03:52:15 2000 Received: from gatekeeper.bnfl.co.uk ([193.35.7.249]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA31946 for ; Tue, 28 Mar 2000 03:52:12 -0500 From: scott.l.owens@bnfl.com Received: by gatekeeper.bnfl.co.uk; id JAA12376; Tue, 28 Mar 2000 09:52:24 +0100 (BST) Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper.bnfl.co.uk via smap (3.2) id xma012360; Tue, 28 Mar 00 09:52:02 +0100 Received: from ASN027.bnfl.com (unverified) by ANT008.SPR.BNFL.COM (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Tue, 28 Mar 2000 09:57:56 +0100 Received: from BNotesMTA1.sell.bnfl.com ([10.10.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id JAA08188 for ; Tue, 28 Mar 2000 09:50:26 +0100 (BST) Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.1 (569.2 2-6-1998)) id 002568B0.00361836 ; Tue, 28 Mar 2000 09:50:51 +0000 X-Lotus-FromDomain: BNFL To: CHEMISTRY@ccl.net Message-Id: <002568B0.0035F553.00@BNotesMTA1.sell.bnfl.com> Date: Tue, 28 Mar 2000 09:50:48 +0000 Subject: MC codes again MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Sorry all - missed one reply from my summary - thanks to Malcolm Gillies "I don't know if it's ideal for your purposes, but you could take a look at Big Mac http://molsim.chem.uva.nl/ It's written in Fortran 77. Unfortunately the source code is not on-line for downloading, but I'm sure the author (Thijs Vlugt) would be glad to help if you send him some email (assuming you want to use it for academic purposes). The Ewald sum implementation doesn't include the correction for non-zero dipole moment." From chemistry-request@server.ccl.net Tue Mar 28 06:53:27 2000 Received: from post.webmailer.de (natmail2.webmailer.de [192.67.198.65]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA01106 for ; Tue, 28 Mar 2000 06:53:26 -0500 Received: from cosmologic.de ([212.144.6.47]) by post.webmailer.de (8.9.3/8.8.7) with ESMTP id NAA11702 for ; Tue, 28 Mar 2000 13:53:15 +0200 (MET DST) Message-ID: <38E09CED.EB02C26D@cosmologic.de> Date: Tue, 28 Mar 2000 13:52:13 +0200 From: "A.Klamt" X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: de MIME-Version: 1.0 To: chemistry@ccl.net Subject: COSMO, COSMO-RS and COSMOtherm Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear colleagues, I am Andreas Klamt, the main author of the solvation methods COSMO and COSMO-RS. By this e-mail I like to inform you about the fact, that after 12 years of Computational Chemistry at Bayer, I have now started my own software and consulting company COSMOlogic. As a result, I am now much more flexible to correspond with people interested in COSMO and COSMO-RS, and you may contact me, if you have questions about these methods. At this occasion I like to inform you about the present state of the programs: 1.) The dielectric continuum solvation model COSMO (COnductorlike Screening MOdel) is available in several quantum chemical programs. I myself collaborated in the implementations in MOPAC (MOPAC7, MOPAC93, ..., MOPAC2000), MNDO, DMol3, GAMESS-US, and TURBOMOLE. Independent implementations, which partly only take the basic idea, but may differ in aspects like cavity construction, outlying charge correction, and scaling function, are: AMPAC, GAUSSIAN98, ADF, and maybe others. 2.) COSMO-RS, i.e. COSMO for Realistic Solvents, has been developed by me after I recognized that the entire dielectric picture of solvents on a moleculare scale is scientifically untenable [A. Klamt, V. Jonas, T. Buerger, J.C.W. Lohrenz, J. Phys. Chem. 102 (1998) 5074]. This method, which - in difference to the macroscopic dielectric continuum methods- describes solute and solvent both on the same footing, starting from COSMO-calculations, allows for realistic calculations of fluid phase thermodynamics, including properties like partition coefficients, solubilities, activity coefficients, vapor pressures, and even phase diagrams. A first implementation of COSMO-RS is available together with DMol3/COSMO from MSI. 3.) COSMOtherm is the latest implementation of COSMO-RS. It is improved in several regards, including: - clearity of input-format - accuracy of temperature dependence - treatment of mult-conformational compounds - quality and breadth of parametrisaions - ... COSMOtherm is able to handle the COSMO-output of DMol3, TURBOMOLE, and MOPAC2000 (although a good semi-empirical parmetrisation is still missing). GAUSSIAN and GAMESS COSMO-output will be handable soon. COSMOtherm is available from COSMOlogic. Looking forward to an interesting time being member of the CCL Andreas Klamt COSMOlogic GmbH&Co.KG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de From chemistry-request@server.ccl.net Tue Mar 28 09:52:05 2000 Received: from ralun.usach.cl (root@ralun.usach.cl [158.170.64.21]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA02047 for ; Tue, 28 Mar 2000 09:51:35 -0500 Received: from lauca.usach.cl ([158.170.51.105]) by ralun.usach.cl (8.10.0.Beta10/8.10.0.Beta10) with ESMTP id e2SEong15423 for ; Tue, 28 Mar 2000 10:50:49 -0400 (CST) Message-ID: <38E0D5DE.54FF6601@lauca.usach.cl> Date: Tue, 28 Mar 2000 11:55:10 -0400 From: danilo2 X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: stability constants for aminoacids/Mn+2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all! I need to find publish stability constants between aminoacids (mainly Glu, His, Gln, Thr, Asn) and Mn+2 I will appreciate any information. Thanks a lot! Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 6811542; 6811644 E-mail : fgonzale@lauca.usach.cl 6811366, Anexo:717 Fax : (562) 681 2108 Fax-Wave: 530-327-8534 ************************************************************************** From chemistry-request@server.ccl.net Tue Mar 28 12:59:39 2000 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA03506 for ; Tue, 28 Mar 2000 12:59:39 -0500 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 12a0Gn-00021F-00 for CHEMISTRY@ccl.net; Tue, 28 Mar 2000 18:59:13 +0100 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 12a0Gj-0001eK-00 for CHEMISTRY@ccl.net; Tue, 28 Mar 2000 18:59:09 +0100 Received: from rzepa.ch.ic.ac.uk ([155.198.234.86]) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 12a0Gi-0077qa-00; Tue, 28 Mar 2000 18:59:08 +0100 Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: Date: Tue, 28 Mar 2000 18:59:04 +0100 To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: Orbital Art Content-Type: text/plain; charset="us-ascii" On a light note, we recently generated lots of unusually shaped molecular orbital images, some of which we thought we would share with the community! The start of our collection is at http://www.ch.ic.ac.uk/photomo/ I challenge people to identify the molecules. If anyone knows of interesting orbital collections out there, do pass the information on. -- Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. http://www.ch.ic.ac.uk/rzepa/ From chemistry-request@server.ccl.net Tue Mar 28 11:28:20 2000 Received: from mallard.duc.auburn.edu (mallard2.duc.auburn.edu [131.204.2.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03066 for ; Tue, 28 Mar 2000 11:28:20 -0500 Received: from localhost (kwonohy@localhost) by mallard.duc.auburn.edu (8.8.8+Sun/8.7.2) with SMTP id KAA07230; Tue, 28 Mar 2000 10:28:02 -0600 (CST) X-Authentication-Warning: mallard.duc.auburn.edu: kwonohy owned process doing -bs Date: Tue, 28 Mar 2000 10:28:02 -0600 (CST) From: Ohyun Kwon X-Sender: kwonohy@mallard To: chemistry@ccl.net cc: APLINCOURT@DRECAM.CEA.FR Subject: summary of solvation models In-Reply-To: <8B4005EFE21AD311936000A0C9FB5BA4831755@kim.saclay.cea.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sorry for late summary of solvation model. The review paper by Cramer and Truhlar is excellent for this topic. : Chem. Rev. 99, 2161-2200 (1999) Thank you for all responses. My original question was; Tue, 15 Feb 2000, Ohyun Kwon wrote: Dear CCLers; I have little experienced about the solvation model caclulation. Would anyone give some suggestions on this matter? Also please recommend which method is effective and best. I will summarize it. Thank you in advance. Ohyun Kwon, graduate Department of Chemistry Auburn Universuty Auburn, AL 36849 USA The resposes are; 1) Two questions arise when you do solvation model calculations in quantum chemistry. One is the availability of an acceptable method and the second the applicability of the results. For example, in Gaussian, you can only do MP2 single point SCRF calculations, while we know MP2 gives better results in gas-phase. True geometry optimizations are possible at the HF and DFT levels, whose applicability is still under constant investigation. (viz. DFT is good for many equilibrium species, its application to the transition states is a million dollar question !!). Selecting choice of method is important and left to question of one's belief, while size consistency in solvents is still an unresolved issue for calculation of activation barriers. Belief of obtained results from single-point SCRF MP2 calculations vs. HF/DFT optimized solvent calculations is in the eye of the behold. Good luck with solvation model calculations. Sree Dr. Sreedhara Rao, Department of Chemistry Washington State University, Pullman, WA 99164. voleti@wsunix.wsu.edu (509)-335-5754 2) Please have a look at Chem. Review, 1999, 99,2161-2200. ------------------------------------- Yongxing Liu Department of Chemistry Wesleyan University Middletown CT 06459 Tel: 860-685-2777 ------------------------------------- 3) You're question is the subject of literally thousands of pages of scientific literature. If you are interested in continuum solvation models, may I suggest the recent review by Don Truhlar and myself ("Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics" Chem. Rev. 1999, 99, 2160). If you are interested in explicit solvent models, a good place to start might be Levy and Gallicchio, Ann. Rev. Phys. Chem. 1998, 49, 531. Older reviews by Jorgensen, Kollman, van Gunsteren, and others are also useful As for which method is "best", such a question cannot be answered without more explanation of what your quality function is. A continuum model will do a lousy job of giving you radial distribution functions, but will save you rather a lot of time if what you really want is Henry's constant for a small organic molecule. CJC From chemistry-request@server.ccl.net Tue Mar 28 19:29:25 2000 Received: from hanno.taiho.co.jp (hanno.taiho.co.jp [210.158.206.38]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA06077 for ; Tue, 28 Mar 2000 19:29:24 -0500 Received: from ishida.taiho.co.jp (dhcp127.taiho.co.jp [210.158.206.123]) by hanno.taiho.co.jp (8.9.3/3.7W) with SMTP id JAA29200 for ; Wed, 29 Mar 2000 09:37:36 +0900 Message-ID: <006001bf8cdf$cdb5c2a0$7bce9ed2@taiho.co.jp> From: "Keisuke Ishida" To: Subject: How to build PC clusters for MD simulation Date: Mon, 13 Mar 2000 20:32:24 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Hi everyone, I want to build PC cluster for MD simulation. Please let me know how to build PC cluster and which MD programs can I get for parallel computers. Thanks. ---------- Keisuke Ishida Chemistry Laboratory, Taiho Pharmaceutical Co.,Ltd. Hanno 357-8527 Japan TEL. +81-429-72-8900 FAX. +81-429-72-8913 E-mail. ishida@taiho.co.jp ---------- From chemistry-request@server.ccl.net Tue Mar 28 20:46:36 2000 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA06448 for ; Tue, 28 Mar 2000 20:46:29 -0500 Received: from lgh ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id JAA05133 for ; Wed, 29 Mar 2000 09:44:50 +0800 (CST) Message-Id: <200003290144.JAA05133@ms.dicp.ac.cn> Date: Fri, 31 Mar 2000 9:47:57 -0800 From: li guo hui Reply-To: chenhua@ms.dicp.ac.cn To: "CHEMISTRY@ccl.net" Subject: about lone pair electron Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear netter: i remembered that someone had given a web address for automatically adding coordination of lone pair electron from file in which there are only coordinations of atoms in CCL, but i forgot it, could you help me about this question or web address? thanks in advance!!!! From chemistry-request@server.ccl.net Tue Mar 28 21:34:07 2000 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA06689 for ; Tue, 28 Mar 2000 21:34:07 -0500 Received: from red5 (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id SAA03721 for ; Tue, 28 Mar 2000 18:34:00 -0800 (PST) Message-Id: <4.2.0.58.20000328184133.00ad79a0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Tue, 28 Mar 2000 18:51:55 -0800 To: CCL From: Laurence Lavelle Subject: Athlon vs Intel performance Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed 1GHz PC's will be shipping in May (Athlon) and June (PIII). Performance comparison: PIII 1GHz with 133MHz bus (anyone know when 200MHz bus is expected ?) vs Athlon 1GHz with 200MHz bus (anyone know of dual Athlon mobo with 200MHz bus ?) Any comments or links would be appreciated. Any comments on CPU comparison of PIII 1GHz vs Athlon 1G (FPU and cache size/speed are the main issues ?). Discussion welcome. Laurence """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Department of Chemistry & Biochemistry and Molecular Biology Institute Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Office): (310) 825-2083 Room 3048A Young Hall Fax: (310) 206-4038 Phone (Lab): (310) 206-8270 Room 269B MBI http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """"""""""""""""