From chemistry-request@ccl.net Wed Nov 26 02:52:41 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQ7q8NL013987 for ; Wed, 26 Nov 2003 02:52:09 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AOuT1-000NGHC; Wed, 26 Nov 2003 08:52 +0100 Message-ID: <3FC454F6.90603/at/chem.vu.nl> Date: Wed, 26 Nov 2003 08:23:34 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Marcin Krol CC: chemistry/at/ccl.net Subject: Re: CCL:Polarization in proteins References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Marcin Krol wrote: > Dear All, > > I am interested in calculating polarization effects (changes in partial > charges) on conformational changes in proteins. I know that there are > many potentials for polarizable water (and other small molecules) models > but I am looking for a (preferably free) program/forcefield that uses > electonegativity equalization method and is parametrized for proteins. > I would also be grateful for any links to relevant papers. I would be very surprised indeed if such a parameterization exists, and by the same token very much interested in seein it, too! AFAIK there are only partially functional implementations for polarization of large molecules in the mainstream simulation software. As for the water models, from what I've heard about that up to now there are still so many (new) questions to answer and issues to adress even for only water, that I don't see people moving on to parametrizing polarizable protein forcefields any time soon. Furthermore, there is still so much to be done on the 'classical' protein forcefields themselves! -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra/at/chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Wed Nov 26 03:00:30 2003 Received: from web1.ulb.ac.be (iee.ulb.ac.be [164.15.59.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQ7xwNL014243 for ; Wed, 26 Nov 2003 02:59:59 -0500 Received: from wwwdev.ulb.ac.be (resu1 [164.15.59.200]) by web1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id IAA18772; Wed, 26 Nov 2003 08:59:58 +0100 (MET) for chemistry)at(ccl.net Date: Wed, 26 Nov 2003 08:59:58 +0100 (MET) Message-Id: <200311260759.IAA18772)at(web1.ulb.ac.be> From: Giju Kalathingal To: chemistry)at(ccl.net Subject: Geometry optimization with BSSE correction X-Mailer: Webmail ULB v2.1 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL-all, Could you please give me info if there is some software available for geometry optimization with BSSE correction? Thanks. Giju Kalathingal Department of General Chemistry (ALGC) Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium. Tel.:++32-2-629-3315 Fax: ++32-2-629-3317 E-mail: Giju.Kalathingal)at(vub.ac.be From chemistry-request@ccl.net Wed Nov 26 05:29:34 2003 Received: from avogadro.kky.ttu.ee (avogadro.kk.ttu.ee [193.40.253.225]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQAT2NL020418 for ; Wed, 26 Nov 2003 05:29:03 -0500 Received: by avogadro.kky.ttu.ee (Postfix, from userid 1000) id 96B322FC5; Wed, 26 Nov 2003 12:29:02 +0200 (EET) Date: Tue, 25 Nov 2003 18:35:31 +0200 From: Toomas Tamm To: VITORGE Pierre 094605 Cc: chemistry!at!ccl.net Subject: Re: CCL:"%mem" trouble of Gaussian Message-ID: <20031125163531.GA11956!at!kky.ttu.ee> References: <3808A7D2DCEAD6118B63009027287265014A20!at!azurite.saclay.cea.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <3808A7D2DCEAD6118B63009027287265014A20!at!azurite.saclay.cea.fr> User-Agent: Mutt/1.3.28i Resent-From: toomas!at!kky.ttu.ee Resent-Date: Wed, 26 Nov 2003 12:29:02 +0200 Resent-To: chemistry!at!ccl.net Resent-Message-Id: <20031126102902.96B322FC5!at!avogadro.kky.ttu.ee> X-Spam-Status: No, hits=-5.2 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,RESENT_TO,USER_AGENT_MUTT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Tue, Nov 25, 2003 at 03:55:44PM +0100, VITORGE Pierre 094605 wrote: > I had similar problems. I run tests with different values for %mem, it seems > there is an optimum %mem value to obtain the shortest CPU time, this optimum > value is usually far from the maximum reasonable value (i.e the amount of > physical memory minus 150to300Mb for the system). This probably depends > (among other reasons) on the size of the exchange file memory, and whether > this file is at the begining of the disk. I asked help to Gaussian, but did > not get any answer. There exists a hypothesis that with today's fast CPU's it is better to re-calculate some integrals in the CPU rather than store and read them > from memory. Integrals are accessed rather randomly and the CPU cannot cache them effectively. A cache miss can cost several tens of CPU cycles while the value is fetched from RAM. It may be faster to re-calculate a simple integral. Thus the calculation is faster if there is less memory available, since this forces the program to re-calculate integrals rather than store them. Can someone with intricate knowledge of modern CPUs and integral calculation algorithms tell if this is true? -- Toomas Tamm e-mail: tt-ccl!at!kky.ttu.ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn Technical University fax: INT+372-620-2020 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From jkl@ccl.net Wed Nov 26 13:32:50 2003 -0500 Return-Path: Reply-To: From: "Mark Thompson" To: chemistry:at:ccl.net Subject: CCL: ArgusLab 4.0 beta #2: critical bug fix available. Date: Wed, 26 Nov 2003 10:19:21 -0800 Message-ID: <000801c3b449$cff1abc0$0200a8c0@planaria> I've fixed a critical bug in ArgusLab (available in 4.0) and made a new installer available on the ArgusLab website. The bug: -------- Occasionally, bonds would simply disappear from a molecule during editing. Furthermore, you could not remake the bond once it disappeared. This bug happened under rare conditions and was hard to reproduce. If you already have installed ArgusLab beta #2, you can simply reinstall over it, or uninstall/reinstall. Thanks for the help from several users on this and apologies for the annoying bug! Sincerely, Mark Thompson *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 mark:at:arguslab.com http://www.arguslab.com *************************** From chemistry-request@ccl.net Wed Nov 26 13:45:57 2003 Received: from relay2.uni-heidelberg.de (relay2.uni-heidelberg.de [129.206.210.211]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQIjPNL009933 for ; Wed, 26 Nov 2003 13:45:25 -0500 Received: from mail.iwr.uni-heidelberg.de (mail.iwr.uni-heidelberg.de [129.206.104.30]) by relay2.uni-heidelberg.de (8.12.10/8.12.10) with ESMTP id hAQIjNSe007850 for ; Wed, 26 Nov 2003 19:45:23 +0100 (MET) Received: from kenzo.iwr.uni-heidelberg.de (IDENT:BgJNQ/K8XJsLrqChW+8r+PfcOSAX0Sfm^at^kenzo.iwr.uni-heidelberg.de [129.206.120.29]) by mail.iwr.uni-heidelberg.de (8.12.10/8.12.9) with ESMTP id hAQIjN8o018493; Wed, 26 Nov 2003 19:45:23 +0100 (MET) Received: from iwr.uni-heidelberg.de (cactus.iwr.uni-heidelberg.de [129.206.120.43]) by kenzo.iwr.uni-heidelberg.de (8.12.8/8.12.8) with ESMTP id hAQIjMH7019080; Wed, 26 Nov 2003 19:45:23 +0100 Message-ID: <3FC4F4C2.1050400^at^iwr.uni-heidelberg.de> Date: Wed, 26 Nov 2003 19:45:22 +0100 From: Matthias Ullmann User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry^at^ccl.net Subject: Free software on ComFA Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, I am looking for free software that can be used for ComFA (comparative field analysis) of small molecules. I am very greatful for any informations. I will make a list and send it to CCL. Best regards, Matthias Ullmann -- ======================================== Prof. Dr. G. Matthias Ullmann Structural Biology/Bioinformatics University of Bayreuth Universitdtsstr. 30, BGI 95447 Bayreuth Germany Telephone: +49-921-55-3545 Fax: +49-921-55-3544 e-mail: Matthias.Ullmann^at^uni-bayreuth.de http://www.bp.uni-bayreuth.de/bisb/ ======================================== From chemistry-request@ccl.net Wed Nov 26 11:32:37 2003 Received: from web15410.mail.cnb.yahoo.com (web15410.mail.cnb.yahoo.com [202.43.216.213]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hAQGW4NL005319 for ; Wed, 26 Nov 2003 11:32:04 -0500 Message-ID: <20031126163154.55052.qmail^at^web15410.mail.cnb.yahoo.com> Received: from [211.138.102.93] by web15410.mail.cnb.yahoo.com via HTTP; Thu, 27 Nov 2003 00:31:54 CST Date: Thu, 27 Nov 2003 00:31:54 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: question about Maximin2 in Sybyl 6.7 To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.4 required=7.0 tests=DATE_IN_PAST_12_24,RCVD_IN_OPM version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, In Sybyl 6.7, I used "log command", and got a script for Maximin2. In the script, the most important command is: MAXIMIN2 M1 Electrostatics IGNORE_ELECTROSTATICS Interesting M1(*-(0)) \ Boundary_Conditions IGNORE_PBCS List DONE INTERACTIVE When I use "take" to submit the script, it works. However, it's interactive, and need me to input "C, G or Q", and later "any key" for the next job. How to change the above line in order to make the calculation is automatic, or non-interactive. B.T.W., don't suggest me to use Netbatch method, I don't like it. Thank you very much for your consideration on this matter. Best regards, Jinsong __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Wed Nov 26 14:16:56 2003 Received: from LaTech.edu (selene.LaTech.edu [138.47.18.25]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQJGPNL011402 for ; Wed, 26 Nov 2003 14:16:25 -0500 Received: from localhost (localhost [127.0.0.1]) by LaTech.edu (Postfix) with ESMTP id 9BABA309BBD for ; Wed, 26 Nov 2003 13:16:25 -0600 (CST) Received: from LaTech.edu ([127.0.0.1]) by localhost (selene.latech.edu [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 42785-01-89 for ; Wed, 26 Nov 2003 13:16:24 -0600 (CST) Received: from helius.latech.edu (helius.LaTech.edu [138.47.18.18]) by LaTech.edu (Postfix) with ESMTP id D2508309BAD for ; Wed, 26 Nov 2003 13:16:24 -0600 (CST) Received: from LAPACHA (unknown [138.47.56.165]) by helius.latech.edu (Postfix) with ESMTP id C428D992C3 for ; Wed, 26 Nov 2003 13:16:24 -0600 (CST) Message-ID: <027b01c3b451$c837b2f0$a5382f8a@LAPACHA> Reply-To: "pderosa-Latech" From: "pderosa-Latech" To: Subject: Tru64 vs. Linux Date: Wed, 26 Nov 2003 13:16:24 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0278_01C3B41F.7D988800" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Virus-Scanned: by amavisd-new at latech.edu X-Spam-Status: No, hits=0.6 required=7.0 tests=HTML_50_60,HTML_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0278_01C3B41F.7D988800 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable How does an Alpha server perform under Linux, compared to Tru64 Unix? = The difference in price is really big but how the performance would be = affected, particularly to run Gaussian. Thanks, Pedro ------=_NextPart_000_0278_01C3B41F.7D988800 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
How does an Alpha server perform under = Linux,=20 compared to Tru64 Unix?  The difference in price is really big but = how the=20 performance would be affected, particularly to run = Gaussian.
 
Thanks,
 
Pedro
------=_NextPart_000_0278_01C3B41F.7D988800-- From chemistry-request@ccl.net Wed Nov 26 13:20:04 2003 Received: from f1n1.spenet.wfu.edu (f1n1.sp2net.wfu.edu [152.17.8.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQIJXNL009072 for ; Wed, 26 Nov 2003 13:19:33 -0500 Received: from wfu.edu (salsbufr-PC.computer.wfu.edu [152.17.84.170]) by f1n1.spenet.wfu.edu (8.11.6p2/8.11.6) with ESMTP id hAQIJXT23196; Wed, 26 Nov 2003 13:19:33 -0500 Message-ID: <3FC4EEB3.3020307)at(wfu.edu> Disposition-Notification-To: freddie salsbury Date: Wed, 26 Nov 2003 13:19:31 -0500 From: freddie salsbury Organization: Wake Forest University User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry)at(ccl.net, natalie)at(wfu.edu Subject: Periodic Boundary Conditions in Gaussian Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) hello -- We're trying to learn how to use the PBC routines in Gaussian 03, and we are reaching a stumbling block with our test case of diamond. If anyone has had much success with PBC in gaussian03 we would appreciate your advice. Our input file, a test case of diamond, with a tiny basis set. (Before we do any real calcs we'd like to understand the simple case.) ------------------------------- %chk=diamond2G.chk %mem=1024MB #HF/STO-3G PBC(NKPoint=48,CellRange=20) Pop(Full) diamond test 0 1 C 0.445875 0.445875 0.445875 C -0.445875 -0.445875 -0.445875 TV 1.7835 1.7835 0.0000 TV 1.7835 0.0000 1.7835 TV 0.0000 1.7835 1.7835 ---------------------------------- First, the gaussian output says it turns symmetry off (even if you turn it on, it cannot identify any symmetry). We varied the CellRange from 20 to 50 and obtained the following results: NClRep CellRange Energy Time (min) MaxNCR NMtPBC Convg 10 -74.8774038316 8.01 285 285 0.3482D-04 15 -74.8788470298 7.40 591 591 0.3388D-04 20 -79.7834971028 335.50 1357 1357 0.1513D-02 25 -77.9532971257 47.78 1717 2179 0.1892D-05 30 -78.4667709573 26.46 1721 3185 0.1067D-04 35 -78.8229423341 32.52 1721 4501 0.7331D-05 40 -78.9686326165 43.85 1721 6775 0.2602D-05 45 -86.8332484908 1479.41 1721 8903 0.2117D-03 50 -83.4676895141 1724.68 1721 11387(convergence failure) (the Cellrange=50 ended with an abnormal termination due to failure to converge) The ones that took a long time to run (20 and 45) not only had large Convg values in the SCF, but also in the population analysis had inequivalent carbons. I'd assume that the energy oscillations are due to the tiny basis set; my chief concerns are with the convergence behavior and understanding the methods. My questions are, and I'd appreciate any assistance with these,: 1) Can one enforce symmetry (space group) in gaussian with PBC? If so, how? 2) What are MaxNCR, NClRep, and NMtPBC ? 3) Why are these parameters be the same for Cellranges <=20, but afterwards the first two level off, while NMtPBC increases between quadratic and cubic 4) Why would the convergence behavior be so erratic? i.e,. some cell ranges seem okay, but some take considerably longer in a seemingly random fashion, with odd results. 5) Does anyone know of any publications or white papers discussing the implementation of PBC in gaussian03? There seems to be virtually no documentation, or citations, in the G03 manual. 6) any suggestions on how to run PBC calcs in G03? thanks for any help you can provide! cheers Fred Dr. Freddie Salsbury, Jr. Assistant Professor Department of Physics Wake Forest University Winston Salem, NC 27109 http://www.wfu.edu/~salsbufr http://csb.wfu.edu/(Center for Structural Biology) From chemistry-request@ccl.net Wed Nov 26 12:52:52 2003 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQHqKNL008165 for ; Wed, 26 Nov 2003 12:52:21 -0500 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Wed, 26 Nov 2003 17:25:13 +0000 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.7p1+Sun/8.9.3) id hAQHPCv27070 for chemistry*at*ccl.net; Wed, 26 Nov 2003 17:25:12 GMT Message-Id: <200311261725.hAQHPCv27070*at*socrates-a.ucl.ac.uk> Subject: CCL: Re: Geometry optimization with BSSE correction To: chemistry*at*ccl.net (CCL) Date: Wed, 26 Nov 2003 17:25:12 +0000 (GMT) In-Reply-To: <200311260759.IAA18772*at*web1.ulb.ac.be> from "Giju Kalathingal" at Nov 26, 2003 08:59:58 AM From: Tanja van Mourik X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Giju, > Could you please give me info if there is some software available > for geometry optimization with BSSE correction? Molpro, for example, can do this. See www.molpro.et. Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik*at*ucl.ac.uk London WC1H 0AJ, UK home: tanja*at*van-mourik.me.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ================================================================= From chemistry-request@ccl.net Wed Nov 26 12:48:48 2003 Received: from mailrelais.univ-rennes1.fr (mailrelais.univ-rennes1.fr [129.20.128.54]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQHmHNL008034 for ; Wed, 26 Nov 2003 12:48:17 -0500 Received: from localhost (localhost [127.0.0.1]) by mailrelais.univ-rennes1.fr (Postfix) with ESMTP id 220A84FF2 for ; Wed, 26 Nov 2003 18:48:17 +0100 (MET) Received: from mailrelais.univ-rennes1.fr ([127.0.0.1]) by localhost (mailrelais.univ-rennes1.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 07208-04 for ; Wed, 26 Nov 2003 18:48:15 +0100 (MET) Received: from mailimailo.univ-rennes1.fr (mailimailo.univ-rennes1.fr [129.20.131.1]) by mailrelais.univ-rennes1.fr (Postfix) with ESMTP id 2A6464FEF for ; Wed, 26 Nov 2003 18:48:15 +0100 (MET) Received: from localhost (localhost [127.0.0.1]) by mailimailo.univ-rennes1.fr (Postfix) with ESMTP id 0332919CC for ; Wed, 26 Nov 2003 18:48:15 +0100 (MET) Received: from mailimailo.univ-rennes1.fr ([127.0.0.1]) by localhost (mailimailo.univ-rennes1.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 03537-01 for ; Wed, 26 Nov 2003 18:48:13 +0100 (MET) Received: from pc138rensc (pc-138-renscr.rech.ensc-rennes.fr [129.20.16.213]) by mailimailo.univ-rennes1.fr (Postfix) with SMTP id B95BF1921 for ; Wed, 26 Nov 2003 18:48:12 +0100 (MET) From: "Sabri Messaoudi" To: Subject: G03 : about ipcm solvation with pseudopotentiels Date: Wed, 26 Nov 2003 18:48:19 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Virus-Scanned: by amavisd-new at univ-rennes1.fr X-Virus-Scanned: by amavisd-new at univ-rennes1.fr X-Spam-Status: No, hits=-0.4 required=7.0 tests=MSGID_GOOD_EXCHANGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I've tried four calculations on optimized NH4+ with C1 symmetry using G03: 1 - 6-31G* Basis 2 - 6-31G* Basis and IPCM solvation model 3 - CEP-31G* Basis 4 - CEP-31G* Basis and IPCM solvation model I obtained theses results for the energies: 1 - gas phase energy=-56.893 2 - gas phase energy=-56.893 energy with solvation = -57.029 3 - gas phase energy=-12.048 4 - gas phase energy=-11.798 energy with solvation = -11.933 I guess that results of 1 and 2 are correct because the gas phase energies are the same with or without the IPCM solvation model. On the other hand using a basis with a pseudopotential CEP in 3 and 4 we obtain DIFFERENT gas phase energies when using or not the IPCM solvation model. In 1 and 2 the energy of solvation is more stable than the gas phase energy but for 3 and 4 it is the opposite. Is it a program error or there is another explanation. Any help ? Thanks in advance. Messaoudi Sabri PHD student ENSC-Rennes FRANCE. sabri.messaoudi*at*univ-rennes1.fr From chemistry-request@ccl.net Wed Nov 26 11:28:53 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQGSMNL005001 for ; Wed, 26 Nov 2003 11:28:22 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HOY000S9WFCSZ*at*mailserver.unimi.it> for chemistry*at*ccl.net; Wed, 26 Nov 2003 17:28:24 +0100 (MET) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HOY00KMEWF88Z*at*smtp.unimi.it> for chemistry*at*ccl.net; Wed, 26 Nov 2003 17:28:20 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 261F514786; Wed, 26 Nov 2003 17:41:12 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 187AC113EE; Wed, 26 Nov 2003 17:41:12 +0100 (CET) Date: Wed, 26 Nov 2003 17:41:10 +0100 (CET) From: Alessandro Contini Subject: Re: CCL:Geometry optimization with BSSE correction In-reply-to: <200311260759.IAA18772*at*web1.ulb.ac.be> To: Giju Kalathingal Cc: chemistry*at*ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 References: <200311260759.IAA18772*at*web1.ulb.ac.be> X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hAQGSsNL005054 Hi, the program GAMESS, available free of charge at http://www.msg.ameslab.gov/GAMESS/GAMESS.html is able to calculate the BSSE correction through the routine SCF-MI (see ref E. Gianinetti et al. J. Quantum Chem, 60, 157 (1996)). Althoug the SCFMI is limited to two monomers at the RHF level. Alessandro Contini On Wed, 26 Nov 2003, Giju Kalathingal wrote: > Dear CCL-all, > > Could you please give me info if there is some software available > for geometry optimization with BSSE correction? > > Thanks. > Giju Kalathingal > > Department of General Chemistry (ALGC) > Vrije Universiteit Brussel > Pleinlaan 2, 1050 Brussels, Belgium. > Tel.:++32-2-629-3315 Fax: ++32-2-629-3317 > E-mail: Giju.Kalathingal*at*vub.ac.be > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY*at*ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST*at*ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl*at*ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini*at*unimi.it From chemistry-request@ccl.net Wed Nov 26 16:47:52 2003 Received: from smtp1.utdallas.edu (smtp1.utdallas.edu [129.110.10.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAQLlLNL016334 for ; Wed, 26 Nov 2003 16:47:21 -0500 Received: from utdallas.edu (pascal.utdallas.edu [10.110.22.68]) by smtp1.utdallas.edu (Postfix) with ESMTP id 705BC389619 for ; Wed, 26 Nov 2003 15:47:21 -0600 (CST) Sender: wfisher/at/utdallas.edu Message-ID: <3FC51EF8.DB7DA1D5/at/utdallas.edu> Date: Wed, 26 Nov 2003 15:45:28 -0600 From: Wayne Fisher X-Mailer: Mozilla 4.79 [en] (X11; U; HP-UX B.11.11 9000/785) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry/at/ccl.net" Subject: CCL:G03 PCM Error Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Colleagues, Occasionally when running a G03 pcm calculation on a molecule I get an abnormal termination with an error message like the following. United Atom Topological Model (UA0 parameters set). UA0: Hydrogen 5 has 3 bounds. Keep it explicit at all point on the UA0: potential energy surface to get meaningful results. Can anyone tell me how to fix this problem? How do I keep an atom explicit? Thanks, Wayne Fisher The University of Texas at Dallas