From chemistry-request@server.ccl.net Wed Dec 19 18:46:07 2001 Received: from france.chem.duke.edu ([152.3.169.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJNk7q12050 for ; Wed, 19 Dec 2001 18:46:07 -0500 Received: from yang3.chem.duke.edu (yang5.chem.duke.edu [152.3.169.205]) by france.chem.duke.edu (8.9.3/8.9.3) with SMTP id SAA04784 for ; Wed, 19 Dec 2001 18:45:46 -0500 (EST) From: Hong Organization: Duke Unversity To: chemistry@ccl.net Subject: questions related with DIIS Date: Wed, 19 Dec 2001 18:28:19 -0500 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <0112191845530B.05777@yang3.chem.duke.edu> Content-Transfer-Encoding: 8bit Dear CCLers, I am using Pulay's DIIS method to accelerate the SCF convergence in my Kohn-Sham codes, and I have several questions concerned with its implementations. How many previous vectors ( density in my case) should be used to get optimal efficiency? Is the DIIS equations always solvable, which I means, is it possible that the set of linear equations become linear-dependent? I also found in some cases some coefficients are negative especially when the number of vectors is small. Is that reasonable? I found if I use the output density as the next input density directly whenever there are negative coefficients, the total performance is better. I guess such problems have been investigated by some researchers, but I don't know where to find the relevant papers. The only paper about DIIS I have at hand is Pulay's (1982 CPL). Would you give me some advices? I appreciate your help! Hong From chemistry-request@server.ccl.net Wed Dec 19 22:46:01 2001 Received: from web15003.mail.bjs.yahoo.com ([61.135.128.6]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fBK3k0q20863 for ; Wed, 19 Dec 2001 22:46:00 -0500 Message-ID: <20011220034533.82842.qmail@web15003.mail.bjs.yahoo.com> Received: from [218.2.137.75] by web15003.mail.bjs.yahoo.com via HTTP; Thu, 20 Dec 2001 11:45:33 CST Date: Thu, 20 Dec 2001 11:45:33 +0800 (CST) From: =?gb2312?q?yong=20pei?= Subject: MD at constant temperature To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear sir Now, I perform a MD simulation of atomic system at constant temperature with Nose-Hoover scheme (Molec. Phys.52, 255, 1984.).The gear predict-corrector method was used . ,Then, how can I determine the initial values of s.derivate of s in the formular? Regards, yong Pei _________________________________________________________ Do You Yahoo!? µÇ¼Ãâ·ÑÑÅ»¢µçÓÊ! http://mail.yahoo.com.cn ÎÞÁÄ£¿ÓôÃÆ£¿¸ßÐË£¿Ã»ÀíÓÉ£¿¶¼À´ÁÄÌì°É£¡¡ª¡ª ÑÅ»¢È«ÐÂÁÄÌìÊÒ! http://cn.chat.yahoo.com/c/roomlist.html From chemistry-request@server.ccl.net Wed Dec 19 18:17:37 2001 Received: from munin.compchem.ucsf.EDU ([128.218.68.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBJNHaq10954 for ; Wed, 19 Dec 2001 18:17:36 -0500 Received: from localhost (pradipta@localhost) by munin.compchem.ucsf.EDU (8.10.2/8.10.2) with ESMTP id fBJNHEJ05992 for ; Wed, 19 Dec 2001 15:17:14 -0800 (PST) Date: Wed, 19 Dec 2001 15:17:14 -0800 From: PostDoc To: Subject: Overdetermined systems of linear equations! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am trying to solve an overdetermined systems of linear equations : (A) m-by-n (X)n = (B)m m > n I am using the 'dgels.f' routine from LAPACK. I am getting strage numbers for a matrix made up by me. I am wondering if anyone has (or point me to) a small matrix, for which the answer is verified. I can then use that matrix to check my code. Ideally n=m-1 for my case. Thanks. Pradipta From chemistry-request@server.ccl.net Thu Dec 20 06:50:30 2001 Received: from c0mailgw09.prontomail.com ([209.185.149.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKBoMq00876 for ; Thu, 20 Dec 2001 06:50:30 -0500 Received: from c0web109 (209.185.149.10) by c0mailgw09.prontomail.com (NPlex 5.5.029) id 3C2119300003B2D8 for chemistry@ccl.net; Thu, 20 Dec 2001 03:42:36 -0800 From: "nahoko matsuzawa" Message-Id: Date: Thu, 20 Dec 2001 03:42:36 -0800 X-Priority: Normal Content-Type: text/plain; charset=ISO-8859-1 To: chemistry@ccl.net Subject: LJ forcefield for K+ X-Mailer: Web Based Pronto Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Dear all, does anybody has a LJ potential for the K+ cation, I want to simulate an aqueous solution containing the K+ ion. I know of a reference Physica B & C 1985, 131, 196, but it is out of reach. thank you very much in advance nahoko ________________________________________________________________ To get your free Web-based E-mail go to http://www.nandomail.com From chemistry-request@server.ccl.net Thu Dec 20 03:03:40 2001 Received: from secure.webhotel.net ([195.41.202.80]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fBK83Zq30392 for ; Thu, 20 Dec 2001 03:03:35 -0500 Received: (qmail 6988614 invoked from network); 20 Dec 2001 08:06:01 -0000 Received: from mail-gateway.webhotel.net (195.41.202.215) by mail.webhotel.net with SMTP; 20 Dec 2001 08:06:01 -0000 X-Authenticated-Timestamp: 09:06:01(CET) on December 20, 2001 Date: Thu, 20 Dec 2001 09:03:12 +0100 (CET) From: Kenneth Geisshirt Sender: kneth@albert.netgroup.dk Reply-To: kenneth@geisshirt.dk To: chemistry@ccl.net Subject: Re: CCL:MD at constant temperature In-Reply-To: <20011220034533.82842.qmail@web15003.mail.bjs.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso-8859-1 Content-Transfer-Encoding: 8BIT On Thu, 20 Dec 2001, [gb2312] yong pei wrote: > The gear predict-corrector method was used . Why don't you use a symplectic algorithm? A symplectic algorithm is typical numerically more stable and predictor-corrector methods. > Then, how can I determine the initial > values of s.derivate of s in the formular? I would begin with s = 0 and take a few steps with a simple integrator. Btw, you're more than welcome to download my old MD software and take a look at my Nose-Hoover implementation or read my Ph.D. thesis (there is a chapter on numerical algorithms): http://kenneth.geisshirt.dk/software/mdreac.tar.gz http://kenneth.geisshirt.dk/publications/phd-thesis.ps.gz Kneth -- Kenneth Geisshirt, M.Sc., Ph.D. http://kenneth.geisshirt.dk Grøndals Parkvej 2A, 3. sal kenneth@geisshirt.dk DK-2720 Vanløse +45 38 87 78 38 From chemistry-request@server.ccl.net Thu Dec 20 09:20:21 2001 Received: from indigo.cs.bgu.ac.il (root@[132.72.42.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKEKLq03085 for ; Thu, 20 Dec 2001 09:20:21 -0500 Received: from cs.bgu.ac.il (phd301b [132.72.42.222]) by indigo.cs.bgu.ac.il (8.11.0/8.11.0) with ESMTP id fBKEJWV07236 for ; Thu, 20 Dec 2001 16:19:32 +0200 (IST) Sender: nomsiew@cs.bgu.ac.il Message-ID: <3BFA659D.AD9BD2CF@cs.bgu.ac.il> Date: Tue, 20 Nov 2001 16:15:57 +0200 From: Naomi Siew X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.3-20mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: protein lengths Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am looking for a list of protein families and their corresponding length (average length, minimal length, or length range). Would appreciate any reference to such a list, Thanks, Naomi From chemistry-request@server.ccl.net Thu Dec 20 09:44:45 2001 Received: from zcsn04.astrazeneca.com ([193.128.1.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKEijq03501 for ; Thu, 20 Dec 2001 09:44:45 -0500 Received: from zcsn14.ukhx.astrazeneca.net (zcsn14.ukhx.astrazeneca.net [192.168.199.14]) by zcsn04.astrazeneca.com (8.9.3/8.9.3.DEF) with ESMTP id OAA04470 for ; Thu, 20 Dec 2001 14:44:22 GMT Received: from zcsn24.ukhx.astrazeneca.net (zcsn24.ukhx.astrazeneca.net [156.71.11.98]) by zcsn14.ukhx.astrazeneca.net (8.9.3/8.9.3) with ESMTP id OAA24926 for ; Thu, 20 Dec 2001 14:40:08 GMT Received: from ukapzcmsxhub01.ukap.astrazeneca.net (ukapzcmsxhub01.ukap.astrazeneca.net [156.71.158.135]) by zcsn24.ukhx.astrazeneca.net (8.10.1/8.10.1) with ESMTP id fBKEe7X18567 for ; Thu, 20 Dec 2001 14:40:07 GMT Received: by ukapzcmsxhub01.ukap.astrazeneca.net with Internet Mail Service (5.5.2650.21) id ; Thu, 20 Dec 2001 14:40:07 -0000 Message-ID: <9FE9B85A29CDD511883D0002A53FF21A0B76F6@INBGCASMSX01> From: "Parthiban, Srinivasan" To: "'CHEMISTRY@ccl.net'" Subject: chemical inventory system pro, CIS Date: Thu, 20 Dec 2001 09:41:23 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Dear CCL, Merry Christmas and Happy New Year 2002. I would like to get your experience on "Chemical inventory system Pro, CIS." Has anybody reviewed/evaluated this software. I would like to receive such reports or your experience. Is this software compatible with ISIS? Please send me your experience. Thanks in advance. - Parthiban S From chemistry-request@server.ccl.net Thu Dec 20 10:16:20 2001 Received: from gip.u-picardie.fr ([193.49.184.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKFGKq04010 for ; Thu, 20 Dec 2001 10:16:20 -0500 Received: from u-picardie.fr (akil.sa.u-picardie.fr [195.83.150.158]) by gip.u-picardie.fr (Postfix) with ESMTP id 830727F61 for ; Thu, 20 Dec 2001 16:15:57 +0100 (CET) Sender: fyd@u-picardie.fr Message-ID: <3C21FEBC.6A3174C6@u-picardie.fr> Date: Thu, 20 Dec 2001 16:07:40 +0100 From: Francois Dupradeau X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Proline residue Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, I guess the effect of aminoacid/proline mutation is well known; in particular, the effects of proline introduction in an alpha-helix and in a beta sheet. Could you give me some references that could explain these effects ? Thanks, Sincerely Yours, Francois From chemistry-request@server.ccl.net Thu Dec 20 10:16:34 2001 Received: from mail.mclink.it ([195.110.128.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKFGXq04028 for ; Thu, 20 Dec 2001 10:16:33 -0500 Received: from k7 (net138-076.mclink.it [195.110.138.76]) by mail.mclink.it (8.11.0/8.9.0) with SMTP id fBKFG9123490 for ; Thu, 20 Dec 2001 16:16:09 +0100 (CET) From: "Elena Fioravanzo" To: "CCL" Subject: R: Q2 Date: Thu, 20 Dec 2001 16:18:59 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Importance: Normal In-Reply-To: <3.0.6.32.20011217161350.007b95a0@cpbnc01.mail.uni-tuebingen.de> I know a program for LINUX called Q2 written at the university of Perugia (group of Sergio Clementi and Gabriele Cruciani, Laboratory for chemometrics, Chemistry department). Maybe you can find it at the University web site, the adress will be something like www.unipg.it I hope this will help you Elena ------------------------------------------------------ dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. Via Salvemini 9 I-36100 Vicenza Italy - Europe Voice ++39 0444 240341 Mobile ++39 347 4054991 Fax ++39 0444 533954 E-mail support@s-in.it Web http://www.s-in.it/ -----Messaggio originale----- Da: Computational Chemistry List [mailto:chemistry-request@ccl.net]Per conto di Christoph Nimptsch Inviato: lunedì 17 dicembre 2001 16.14 A: chemistry@ccl.net Oggetto: CCL:Q2 Dear CCLers, recently I was looking for a free program for linux that can do PLS and PCA analysis and I found Q2. Apparently, the links were broken and I was unable to find a source for it. Do anyone know what happened to Q2 and where to download it? Thanks, Christoph Nimptsch ------------------------------------------ Christoph Nimptsch Apotheker Pharmazeutisches Institut Arbeitskreis Prof. Kovar Universität Tübingen Auf der Morgenstelle 8 D-72076 Tuebingen Tel.: 07071/2978794 mailto:christoph.nimptsch@uni-tuebingen.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 From chemistry-request@server.ccl.net Thu Dec 20 09:07:10 2001 Received: from post.tau.ac.il ([132.66.16.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKE79q02818 for ; Thu, 20 Dec 2001 09:07:09 -0500 Received: from post.tau.ac.il (pico.tau.ac.il [132.66.145.20]) by post.tau.ac.il (8.11.6/8.11.6) with ESMTP id fBKE6gw17066 for ; Thu, 20 Dec 2001 16:06:42 +0200 (IST) Sender: silviu@post.tau.ac.il Message-ID: <3C21F06C.D7475569@post.tau.ac.il> Date: Thu, 20 Dec 2001 14:06:36 +0000 From: Zilberman Silviu Organization: TAU X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.10 i686) X-Accept-Language: en MIME-Version: 1.0 To: ccl Subject: molecular viewer Content-Type: multipart/mixed; boundary="------------E9A6A95E1922E1B1E38BC74D" This is a multi-part message in MIME format. --------------E9A6A95E1922E1B1E38BC74D Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone, I am looking for a way to dispaly MD snapshots such that the coloring of the atoms would reflect the value of their z coordinate. Thanks, Silviu. -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu School of Chemistry, Tel Aviv University Ramat Aviv, Tel-Aviv, Israel 61391 Phones 972-3-6407634 (office) 972-3-6409293 (fax 1 - School of Chemistry) 972-3-6423765 (fax 2 - Prof. A. Nitzan) mailto:silviu@post.tau.ac.il Home Page: http://femto.tau.ac.il/~silviu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --------------E9A6A95E1922E1B1E38BC74D Content-Type: text/x-vcard; charset=us-ascii; name="silviu.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Zilberman Silviu Content-Disposition: attachment; filename="silviu.vcf" begin:vcard n:Zilberman;Silviu tel;work:972-3-6407634 x-mozilla-html:TRUE org:Tel Aviv University;School of Chemistry version:2.1 email;internet:silviu@post.tau.ac.il adr;quoted-printable:;;Tel Aviv University=0D=0ASchool of Chemistry;Tel Aviv;;69978;Israel x-mozilla-cpt:;-17216 fn:Silviu Zilberman end:vcard --------------E9A6A95E1922E1B1E38BC74D-- From chemistry-request@server.ccl.net Thu Dec 20 10:30:08 2001 Received: from popserver.healthtech.com ([140.239.39.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKFU7q04355 for ; Thu, 20 Dec 2001 10:30:07 -0500 Received: by popserver.healthtech.com from localhost (router,SLMail V4.3); Thu, 20 Dec 2001 10:33:06 -0500 for Received: from edelo [140.239.39.147] by popserver.healthtech.com [140.239.39.130] (SLmail 4.3.0.3454) with SMTP id 4AD347819EDD47C9B63258819CD55097 for ; Thu, 20 Dec 2001 10:33:05 -0500 Message-Id: <4.1.20011220101926.00a14f00@140.239.39.130> X-Sender: eoregan@140.239.39.130 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 20 Dec 2001 10:25:27 -0500 To: chemistry@ccl.net From: "Edel O'Regan" Subject: Exploiting Molecular Diversity conference Feb. 2002 San Diego Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_6255214==_.ALT" X-SLUIDL: BCE5E250-E85A409C-9E0F3C91-A0A48445 --=====================_6255214==_.ALT Content-Type: text/plain; charset="us-ascii" Announcing Cambridge Healthtech Institute's Exploiting Molecular Diversity conference http://www.healthtech.com/2002/mld/index.htm Edel O'Regan Ph.D. Conference Producer Cambridge Healthtech Institute FAX: 617-630-1325 Phone: 617-630-1323 email: eoregan@healthtech.com --=====================_6255214==_.ALT Content-Type: text/html; charset="us-ascii" Announcing Cambridge Healthtech Institute's Exploiting Molecular Diversity conference

                http://www.healthtech.com/2002/mld/index.htm



Edel O'Regan Ph.D.
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Cambridge Healthtech Institute
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email: eoregan@healthtech.com --=====================_6255214==_.ALT-- From chemistry-request@server.ccl.net Thu Dec 20 10:50:11 2001 Received: from indigo.cs.bgu.ac.il (root@[132.72.42.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKFoAq04932 for ; Thu, 20 Dec 2001 10:50:10 -0500 Received: from cs.bgu.ac.il (phd301b [132.72.42.222]) by indigo.cs.bgu.ac.il (8.11.0/8.11.0) with ESMTP id fBKFnLV26760 for ; Thu, 20 Dec 2001 17:49:21 +0200 (IST) Sender: nomsiew@cs.bgu.ac.il Message-ID: <3BFA7AAA.5B081DB5@cs.bgu.ac.il> Date: Tue, 20 Nov 2001 17:45:46 +0200 From: Naomi Siew X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.3-20mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: protein lengths Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I would like to rephrase my question: I am looking for a list of protein families, by function (e.g. GPCRs, ribozomes, immunoglobulins, Ser proteases, etc.), and their lengths. e.g. GPCRs - average length xxx residues (or: length range: xxx-yyy residues), etc. I am most interested to know which are the longest proteins. Those functional databases that I searched give a general length distribution for each organism. Perhaps I missed those that have a general length distribution, by function, for all the organisms sequenced thus far. Thanks, Naomi From chemistry-request@server.ccl.net Thu Dec 20 16:03:13 2001 Received: from web9604.mail.yahoo.com ([216.136.129.183]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fBKL3DS02227 for ; Thu, 20 Dec 2001 16:03:13 -0500 Message-ID: <20011220210245.79971.qmail@web9604.mail.yahoo.com> Received: from [192.187.17.2] by web9604.mail.yahoo.com via HTTP; Thu, 20 Dec 2001 13:02:45 PST Date: Thu, 20 Dec 2001 13:02:45 -0800 (PST) From: Xavier Girones Subject: Solvation in Gaussian within AM1 To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL-clients, Is there any way to similate solvent effects with Gaussian within the AM1 level of theory? I have been browsing the manual, and it seems that solvation is only available for HF methods and above. Any cue? Xavier Gironés Institute of Computational Chemistry University of Girona Girona, Spain __________________________________________________ Do You Yahoo!? Check out Yahoo! Shopping and Yahoo! Auctions for all of your unique holiday gifts! Buy at http://shopping.yahoo.com or bid at http://auctions.yahoo.com From chemistry-request@server.ccl.net Thu Dec 20 17:18:12 2001 Received: from strontium.biochem.du.edu ([130.253.176.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKMI8S03839 for ; Thu, 20 Dec 2001 17:18:12 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by strontium.biochem.du.edu (8.11.6/8.11.6) id fBKMGo004886 for chemistry@ccl.net; Thu, 20 Dec 2001 15:16:50 -0700 Content-Type: text/plain; charset="iso-8859-1" From: Jim Stoner Reply-To: jstoner@du.edu To: chemistry@ccl.net Subject: G98 A11.1 >> %MEM=xxx,yyy Date: Thu, 20 Dec 2001 15:16:49 -0700 X-Mailer: KMail [version 1.2] MIME-Version: 1.0 Message-Id: <01122015164900.04867@strontium.biochem.du.edu> Content-Transfer-Encoding: 8bit Hi All: Quick question. Upon inspection of a G98 test file I found: %chk=test322 %mem=2000000,4000000 #p RHF/STO-3G test opt freq Gaussian Test Job 322 (Part 1): C60 Icosahedral Which makes sense, except for the %mem card. What exactly is going on here with the dual specification of memory allocation. This is not in the G98 user's guide nor is it on the website so I am at a bit of a loss... Thanks Jim ======================================= James Stoner Graduate Student Eaton Paramagenetics Laboratories University of Denver Department of Chemistry and Biochemistry ======================================= From chemistry-request@server.ccl.net Thu Dec 20 17:42:35 2001 Received: from adenine.cgl.ucsf.edu ([128.218.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKMgZS04124 for ; Thu, 20 Dec 2001 17:42:35 -0500 Received: from adenine.cgl.ucsf.edu (localhost [127.0.0.1]) by adenine.cgl.ucsf.edu (8.12.1/8.12.1/GSC1.10) with ESMTP id fBKMg7fc669495; Thu, 20 Dec 2001 14:42:07 -0800 (PST) Received: (from ross@localhost) by adenine.cgl.ucsf.edu (8.12.1/8.12.1/Submit) id fBKMg58b669490; Thu, 20 Dec 2001 14:42:05 -0800 (PST) Date: Thu, 20 Dec 2001 14:42:05 -0800 (PST) From: Bill Ross Message-Id: <200112202242.fBKMg58b669490@adenine.cgl.ucsf.edu> To: chemistry@ccl.net, nahoko@nandomail.com Subject: Re: CCL:LJ forcefield for K+ does anybody has a LJ potential for the K+ cation, I want to simulate an aqueous solution containing the K+ ion. I know of a reference Physica B & C 1985, 131, 196, but it is out of reach. It depends on the water model, and also on the combining rules used for mixing the LJ with the water LJ. See Ross, W.S. and Hardin, C.C., J. Am. Chem. Soc. 116, 6070-6080 (1994). We discovered that various parameters seem to work equally well. The commonly-used parameters for K+ are those of Aqvist, but simpler ones give indistinguishable results for free energy and radial distribution. We also had to convert the Aqvist parameters for use with the combining rules used in the Amber programs. And different parameters were necessary for ion interactions with non-TIP3 atoms. Bill Ross From chemistry-request@server.ccl.net Thu Dec 20 18:25:17 2001 Received: from adenine.cgl.ucsf.edu ([128.218.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKNPHS04585 for ; Thu, 20 Dec 2001 18:25:17 -0500 Received: from localhost (socrates.cgl.ucsf.edu [128.218.27.3]) by adenine.cgl.ucsf.edu (8.12.1/8.12.1/GSC1.10) with ESMTP id fBKNOqfd672346 for ; Thu, 20 Dec 2001 15:24:52 -0800 (PST) Date: Thu, 20 Dec 2001 15:24:52 -0800 (PST) From: Pradipta Bandyopadhyay To: chemistry@ccl.net Subject: Using SVD in LAPACK! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am using DGELSS.F (which used singular value decomposition) from LAPACK to solve my overdetermined linear system of equations. It seems I can not call the routine properly, because I am getting incorrect answer. The question is : what to use for RCOND and LWORK when I call DGELSS? Has anybody used this routine successfully? Thanks. Pradipta From chemistry-request@server.ccl.net Thu Dec 20 17:22:13 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBKMMDS03901 for ; Thu, 20 Dec 2001 17:22:13 -0500 Received: from silicon.chem.ucla.edu (silicon.chem.ucla.edu [169.232.135.10]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id fBKMLlT24225; Thu, 20 Dec 2001 14:21:47 -0800 (PST) Received: from localhost (mdb@localhost) by silicon.chem.ucla.edu (8.11.1/8.11.1) with ESMTP id fBKMLuJ03029; Thu, 20 Dec 2001 14:21:56 -0800 (PST) X-Authentication-Warning: silicon.chem.ucla.edu: mdb owned process doing -bs Date: Thu, 20 Dec 2001 14:21:56 -0800 (PST) From: "Michael D. Bartberger" To: Xavier Girones cc: Subject: Re: CCL:Solvation in Gaussian within AM1 In-Reply-To: <20011220210245.79971.qmail@web9604.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id fBKMMDS03902 Hello Xavier: If you are interested in solvation energies computed from semi-empirical based wavefunctions, you may wish to look into the AMSOL package developed by Cramer and coworkers at the University of Minnesota. Regards, -Mike On Thu, 20 Dec 2001, Xavier Girones wrote: > Dear CCL-clients, > > Is there any way to similate solvent effects with > Gaussian within the AM1 level of theory? I have been > browsing the manual, and it seems that solvation is > only available for HF methods and above. Any cue? > > Xavier Gironés > Institute of Computational Chemistry > University of Girona > Girona, Spain > > __________________________________________________ > Do You Yahoo!? > Check out Yahoo! Shopping and Yahoo! Auctions for all of > your unique holiday gifts! Buy at http://shopping.yahoo.com > or bid at http://auctions.yahoo.com > > > -= 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 > > > > >