From chemistry-request@ccl.net Fri Dec 5 03:57:42 2003 Received: from vimg1.rdg.ac.uk (vimg1.rdg.ac.uk [134.225.1.81]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB58vAxp018211 for ; Fri, 5 Dec 2003 03:57:10 -0500 Received: from vimp2.rdg.ac.uk ([134.225.16.91]) by vimg1.rdg.ac.uk (Exim: gateway) with esmtp id 1ASBlu-0005SD-00 for chemistry-.at.-ccl.net; Fri, 05 Dec 2003 08:57:10 +0000 Received: from vimh1.rdg.ac.uk ([134.225.16.83]) by vimp2.rdg.ac.uk (Exim: virusscanner) with esmtp id 1ASBln-0007w3-00 for chemistry-.at.-ccl.net; Fri, 05 Dec 2003 08:57:03 +0000 Received: from scpc146.rdg.ac.uk ([134.225.169.246] helo=scpc146) by vimh1.rdg.ac.uk (Exim: host) with smtp id 1ASBln-0004cz-00; Fri, 05 Dec 2003 08:57:03 +0000 Message-ID: <004d01c3bb0d$c3e24220$f6a9e186-.at.-rdghome.ad.rdg.ac.uk> From: "Tris Youngs" To: "Joslyn Kravitz" , References: <002501c3baa2$ec1abf30$80e12844@Garfield> Subject: Re: CCL:windows based orbital viewing Date: Fri, 5 Dec 2003 08:57:09 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_004A_01C3BB0D.C3CE6C00" 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-Scanner: exiscan *1ASBln-0007w3-00*Lf15uK1a4to* (The University of Reading) X-Spam-Status: No, hits=0.1 required=7.0 tests=HTML_80_90,HTML_MESSAGE,REFERENCES 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_004A_01C3BB0D.C3CE6C00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Molekel (http://www.cscs.ch/molekel/) is an excellent, and free, = solution. Tris Youngs. ----- Original Message -----=20 From: Joslyn Kravitz=20 To: chemistry-.at.-ccl.net=20 Sent: Thursday, December 04, 2003 8:12 PM Subject: CCL:windows based orbital viewing Hello all, =20 Does anyone know of viewing program that can display molecular = orbitals from Gaussian output? I am looking for something that runs on = windows and preferably is free. =20 Thanks, Joslyn Kravitz ------=_NextPart_000_004A_01C3BB0D.C3CE6C00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Molekel (http://www.cscs.ch/molekel/) is = an=20 excellent, and free, solution.

Tris Youngs.

----- Original Message -----
From:=20 Joslyn=20 Kravitz
To: chemistry-.at.-ccl.net

Sent: Thursday, December 04, = 2003 8:12=20 PM

Subject: CCL:windows based = orbital=20 viewing

Hello=20 all,

Does anyone know of = viewing=20 program that can display molecular orbitals from=20 Gaussian output? I am looking for something that runs on windows and=20 preferably is free.

Thanks,

Joslyn=20 Kravitz

------=_NextPart_000_004A_01C3BB0D.C3CE6C00-- From chemistry-request@ccl.net Fri Dec 5 03:31:44 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 hB58VDxp017288 for ; Fri, 5 Dec 2003 03:31:13 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1ASAg9-000NGtC; Fri, 5 Dec 2003 08:47 +0100 Message-ID: <3FCF7449.7070205[at]chem.vu.nl> Date: Thu, 04 Dec 2003 18:52:09 +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: FyD CC: chemistry[at]ccl.net Subject: Re: CCL:Hydrogen bonds References: <1070511302.3fceb4c631282[at]webmail.u-picardie.fr> In-Reply-To: <1070511302.3fceb4c631282[at]webmail.u-picardie.fr> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.1 required=7.0 tests=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) FyD wrote: > Dear All, > > I am looking for references describing intra or inter-molecular Hydrogen bonds (life time for > example) observed in small organic molecules, peptides or nucleic acids during ... some > experiments (for instance during molecular dynamics simulations). In J. Biomol. NMR 23, 181-194, 2002 (Table 2) I report hydrogen bond lifetimes in a *nonapeptide* during MD simulations of 200-700 ns (!). In J. Comput. Chem. 20 (8), pp 786-798, 1999 (Table II) I report intra-molecular h-bond lifetimes in *liquid* *water*, also from MD simulations. In J. Phys. Chem. B 106, 8858-8869, 2002 (Figure 3, and description in text) we describe hydrogen bonding *networks* in *FAD* (flavin-adenine-dinucleotide), although no lifetimes were determined. Hope this helps you along a bit... -- 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 Fri Dec 5 08:52:45 2003 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB5DqDxp027874; Fri, 5 Dec 2003 08:52:13 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id hB5DqBjm003038; Fri, 5 Dec 2003 08:52:11 -0500 Date: Fri, 5 Dec 2003 08:52:11 -0500 (EST) From: Jan Labanowski To: chemistry[at]ccl.net cc: jkl[at]ccl.net Subject: ACS Journals new policy discussion Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL, I am being reminded that CCL is not a good forum to discuss recent editorial policies imposed on ACS and other society publishers. Those who know me personally, may easily guess what is my opinion. They should also understand that running the CCL requires my occassional intervention. The discussion on this topic has to be taken off the list or else... While I do not censor messages appearing on CCL, I have added some keywords to the filters hoping that they will remove the traffic on this topic from the general distribution. Please understand that I do not want to win the battle and loose the war... Jan Labanowski CCL Administrator jkl[at]ccl.net From chemistry-request@ccl.net Fri Dec 5 03:31:11 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 hB58Uexp017269 for ; Fri, 5 Dec 2003 03:30:40 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1ASAg7-000NGpC; Fri, 5 Dec 2003 08:47 +0100 Message-ID: <3FCF6FDC.5020409[at]chem.vu.nl> Date: Thu, 04 Dec 2003 18:33:16 +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: "Tarek M. El-Gogary" CC: CHEMISTRY[at]ccl.net Subject: Re: CCL:Molecular Complexes References: <095F5EDC6A006F41AFF7804586108ACF38E4EE[at]mail.mans.edu.eg> In-Reply-To: <095F5EDC6A006F41AFF7804586108ACF38E4EE[at]mail.mans.edu.eg> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,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) Tarek M. El-Gogary wrote: > > > Dear CCLers, > > I am looking for an accurate definition for the term, Molecular Complexes. [...] This would, I'm afraid, be somewhat context dependent. There is a wide, and fairly continues scale of complexes, both terms of affinity (i.e. strength of binding of the partners in the comples) and in lifetime (i.e. persistence times of the binding). In other words, it would depend on the time-window you are interested in, and on the relative affinity with respect to other processes/binding partners/etc. in your sysem of interest. -- 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 Thu Dec 4 21:37:12 2003 Received: from col-msxproto1.col.missouri.edu (col-msxproto1.col.missouri.edu [128.206.3.151]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB52afxp009537 for ; Thu, 4 Dec 2003 21:36:41 -0500 Received: from mizzou.edu ([128.206.124.129]) by col-msxproto1.col.missouri.edu over TLS secured channel with Microsoft SMTPSVC(5.0.2195.6673); Thu, 4 Dec 2003 20:36:40 -0600 Message-ID: <3FCFEF48.9020500[at]mizzou.edu> Disposition-Notification-To: Lorant Janosi Date: Thu, 04 Dec 2003 20:36:56 -0600 From: Lorant Janosi 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, ro, hu MIME-Version: 1.0 To: Computational Chemistry List Subject: ZINDO with point charges included Content-Type: multipart/alternative; boundary="------------080605090709050502040202" X-OriginalArrivalTime: 05 Dec 2003 02:36:40.0684 (UTC) FILETIME=[9D094AC0:01C3BAD8] X-Spam-Status: No, hits=1.2 required=7.0 tests=HTML_20_30,HTML_MESSAGE,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. --------------080605090709050502040202 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCL's, I would like to do some ZINDO calculations on a system that has point charges included. Does anyone know a software that does that, because I know gaussian 98/03 cannot do this (I tried & does not work; g03 is specifiying that this is not possible, too). Or, how could I do some other semiempirical calculations of excited states on a system with point charges? Thanks a lot. Lori. -- Lorant Janosi Department of Physics and Astronomy University of Missouri-Columbia email: lj8q5[at]mizzou.edu --------------080605090709050502040202 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL's,

I would like to do some ZINDO calculations on a system that has point charges included. Does anyone know a software that does that, because I know gaussian 98/03 cannot do this (I tried & does not work; g03 is specifiying that this is not possible, too).
Or, how could I do some other semiempirical calculations of excited states on a system with point charges?

Thanks a lot.
Lori.

-- 
Lorant Janosi
Department of Physics and Astronomy
University of Missouri-Columbia

email: lj8q5[at]mizzou.edu

--------------080605090709050502040202-- From chemistry-request@ccl.net Fri Dec 5 02:47:39 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 hB57l7xp016324 for ; Fri, 5 Dec 2003 02:47:07 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1ASAg6-000NGCC; Fri, 5 Dec 2003 08:47 +0100 Message-ID: <3FCF6F1D.3070304~at~chem.vu.nl> Date: Thu, 04 Dec 2003 18:30:05 +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: Maciej Haranczyk CC: CHEMISTRY~at~ccl.net Subject: Re: CCL:Thermodynamic corrections at MM level (fwd) 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) Maciej Haranczyk wrote: > Dear CCLers, > > I did some DFT (B3LYP) calculations on small DNA fragments (~200atoms). > I would like to calculate thermodynamic corrections (EZPV,H,G) for these > systems but since I do not have fully optimized geometries (I had to > freeze nucleic acid bases layers because B3LYP does not deal with > dispersion (pi-stacking)) I cannot run frequency calculation at B3LYP > level. > I would like to calculate thermodynamic corrections with MM approach and > then add it to B3LYP energies. Since I am not familiar with MM programs > I would be grateful if someone suggested me any free program than can do > that or paper on this topic. I'm not sure if this answers your quistion, but in the MD package Gromacs one can perform what is called 'Quasi Harmonic Entropy' calculations, involving covariance analysis on atomic coordinates and analysis of the resulting eigenvalues that correspond to generalized modes of motion (i.e. the eigenvectors). Gromacs is available for free at www.gromacs.org. There are more Gromacs users (and developers) on the CCL, so you may also get (more appropriate) answers from them...? -- 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 Fri Dec 5 02:37:32 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 hB57axxp016090 for ; Fri, 5 Dec 2003 02:37:00 -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 <0HPE00FZ2VTNKK~at~mailserver.unimi.it> for chemistry~at~ccl.net; Fri, 05 Dec 2003 08:36:59 +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 <0HPE00KPHVTMC1~at~smtp.unimi.it> for chemistry~at~ccl.net; Fri, 05 Dec 2003 08:36:58 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 7F77527197; Fri, 05 Dec 2003 08:40:42 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 780882717D; Fri, 05 Dec 2003 08:40:42 +0100 (CET) Date: Fri, 05 Dec 2003 08:40:40 +0100 (CET) From: Alessandro Contini Subject: Re: CCL:windows based orbital viewing In-reply-to: <002501c3baa2$ec1abf30$80e12844@Garfield> To: Joslyn Kravitz Cc: chemistry~at~ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 References: <002501c3baa2$ec1abf30$80e12844@Garfield> X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hB57bWxp016100 Hi Joslyn, you could try both molekel (http://cscs.ch/molekel/) and molden (http://www.caos.kun.nl/~schaft/molden/molden.html) They are free for non commercial institutions and are able to display orbitals from both gaussian and gamess. Reguards Alessandro Contini On Thu, 4 Dec 2003, Joslyn Kravitz wrote: > Hello all, > > Does anyone know of viewing program that can display molecular orbitals > > from Gaussian output? I am looking for something that runs on windows > and preferably is free. > > Thanks, > Joslyn Kravitz > Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini~at~unimi.it From chemistry-request@ccl.net Fri Dec 5 02:24:28 2003 Received: from dns.lpmc.univ-montp2.fr (dns.lpmc.univ-montp2.fr [162.38.149.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB57Nnxp015745 for ; Fri, 5 Dec 2003 02:23:55 -0500 Received: from localhost (pboulet@localhost) by dns.lpmc.univ-montp2.fr (8.11.6/8.11.6) with ESMTP id hB57MP710438; Fri, 5 Dec 2003 08:22:25 +0100 X-Authentication-Warning: dns.lpmc.univ-montp2.fr: pboulet owned process doing -bs Date: Fri, 5 Dec 2003 08:22:25 +0100 (CET) From: Pascal Boulet X-X-Sender: pboulet:at:dns.lpmc.univ-montp2.fr Reply-To: Pascal.boulet:at:lpmc.univ-montp2.fr To: Joslyn Kravitz cc: chemistry:at:ccl.net Subject: Re: CCL:windows based orbital viewing In-Reply-To: <002501c3baa2$ec1abf30$80e12844@Garfield> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,SIGNATURE_LONG_DENSE,USER_AGENT_PINE, X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, There's Molekel: http://www.cscs.ch/molekel/ and Molden: http://www.cmbi.kun.nl/~schaft/molden/molden.html They are free of charge. hope this help, Pascal On Thu, 4 Dec 2003, Joslyn Kravitz wrote: > Hello all, > > Does anyone know of viewing program that can display molecular orbitals > > from Gaussian output? I am looking for something that runs on windows > and preferably is free. > > Thanks, > Joslyn Kravitz > -- Dr. Pascal Boulet Laboratoire de Physico-chimie de la Matihre Condensie UMR 5617 Universiti de Montpellier II Place Eughne Bataillon 34095 Montpellier Cedex 5 tel. 04 67 14 33 00 Fax 04 67 14 42 90 courriel: Pascal.Boulet:at:lpmc.univ-montp2.fr From chemistry-request@ccl.net Fri Dec 5 01:53:21 2003 Received: from spam.kjist.ac.kr (spam.kjist.ac.kr [203.237.32.199]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hB56qmxp014846 for ; Fri, 5 Dec 2003 01:52:49 -0500 Received: (snipe 25211 invoked by alias); 5 Dec 2003 07:24:34 -0000 Received: from akhlaq95|at|kjist.ac.kr with SpamSniper2.68 (Processed in 0.010232 secs); Received: from unknown (HELO kjist.ac.kr) (203.237.32.200) by 0 with SMTP; 5 Dec 2003 07:24:34 -0000 X-RCPTTO: chemistry|at|ccl.net, Received: (qmail 15052 invoked by uid 10005); 5 Dec 2003 15:40:11 +0900 Received: from akhlaq95|at|kjist.ac.kr by kjist.ac.kr by uid 10002 with qmail-scanner-1.14 (virobot: 2.0/IOL. Clear:. Processed in 0.132008 secs); 05 Dec 2003 06:40:11 -0000 Received: from unknown (HELO kjist.ac.kr) ([203.237.32.200]) (envelope-sender ) by eunhasu.kjist.ac.kr (qmail-ldap-1.03) with SMTP for ; 5 Dec 2003 15:40:11 +0900 Received: from 203.237.43.100 by kjist.ac.kr with HTTP; Fri, 5 Dec 2003 15:40:11 +0900 (KST) Message-ID: <1713.203.237.43.100.1070606411|at|kjist.ac.kr> Date: Fri, 5 Dec 2003 15:40:11 +0900 (KST) Subject: Subject: young's modulus of air From: "Akhalq.Ahmad" To: chemistry|at|ccl.net Reply-To: akhlaq95|at|kjist.ac.kr X-Priority: 5 X-Mailer: BizBaBa WebMail (version 2.0) MIME-Version: 1.0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.3 required=7.0 tests=FROM_ENDS_IN_NUMS,HTML_30_40,HTML_IMAGE_ONLY_04, HTML_MESSAGE,HTML_WEB_BUGS,MAILTO_TO_SPAM_ADDR, MIME_HTML_ONLY version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I want to know th eyoung's modulus of elasticity of Air

Regards
Akhlaq, Ahmad
MEMS&NanoPhotonics lab
Mechatronics Deptt. KwangJu Institute of Science & Technology
1 Oryong-Dong Buk-Gu Gwangju 500-712 Korea
Cell. +82-18-875-1417
Res.# +82-62-970-2777
Off.# +82-62-970-2424
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Homepage:-http://mems.kjist.ac.kr
E-mail:- akhlaq95|at|kjist.ac.kr From chemistry-request@ccl.net Thu Dec 4 22:17:11 2003 Received: from wanderer.mr.itd.umich.edu (wanderer.mr.itd.umich.edu [141.211.93.146]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB53Gdxp010543 for ; Thu, 4 Dec 2003 22:16:39 -0500 Received: from Garfield (pcp05005614pcs.sanarb01.mi.comcast.net [68.40.225.128]) by wanderer.mr.itd.umich.edu (smtp) with ESMTP id hB53GasN014917 for ; Thu, 4 Dec 2003 22:16:39 -0500 From: "Joslyn Kravitz" To: Subject: RE: windows based orbital viewing Date: Thu, 4 Dec 2003 22:16:46 -0500 Message-ID: <000a01c3bade$3a356630$80e12844@Garfield> MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 In-Reply-To: <000d01c3bad5$10f66750$0200a8c0@planaria> X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Well, there certainly are plenty of options out there for people wanting to view orbitals: ArgusLab 4.0 (currently in beta release) integrates well with Gaussain 98 and Gaussian 03. You can easily view surfaces from cube files generated with Gaussian. ArgusLab is free for single-user academic faculty, staff, and students. You can download it at http://www.arguslab.com MOPLOT. http://www-chem.unifr.ch/frames/facilities/moplot/moplot.html It is a free version, but you should use pop=full in the input file. This programe enables you to view the molecular orbitals. This can also be downloaded for linux version also. Molden can display molecular orbitals generated by Gaussian. However even the windows version requires an x server. http://www.cmbi.kun.nl/~schaft/molden/molden.html Cygwin is free and has an x server. WebMO is a free web-based interface to several computational chemistry programs: Gaussian, Mopac, Gamess, and Molpro. The professional version, WebMO Pro, has a windows-based molecular orbital viewer, MOViewer, that allows you to view MO's that were calculated by any of the supported programs. MOViewer also displays isosurfaces, electrostatic potentials, and electrophilic/nucleophilic frontier surfaces. For general information, see the WebMO homepage at www.webmo.net A working demo (no download or installation required, since WebMO is web-based) is available at www.webmo.net/demo Color brochures are at http://www.webmo.net/download/WebMO_Brochure.pdf http://www.webmo.net/download/WebMOPro_Brochure.pdf Thanks for all the advice. I went with gOpenMol: http://www.csc.fi/gopenmol/distribute/index.phtml Joslyn Kravitz From chemistry-request@ccl.net Fri Dec 5 05:26:29 2003 Received: from marilyn.uochb.cas.cz (marilyn.uochb.cas.cz [147.231.120.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB5APvxp021811 for >ccl.net>; Fri, 5 Dec 2003 05:25:58 -0500 Received: from iveta.uochb.cas.cz (iveta.uochb.cas.cz [147.231.120.176]) by marilyn.uochb.cas.cz (8.11.6/8.11.6) with ESMTP id hB5APrk01964 for >ccl.net>; Fri, 5 Dec 2003 11:25:53 +0100 Received: from svozil by iveta.uochb.cas.cz with local (Exim 3.35 #1 (Debian)) id 1ASD9o-0002AX-00 for >ccl.net>; Fri, 05 Dec 2003 11:25:56 +0100 Date: Fri, 5 Dec 2003 11:25:56 +0100 To: chemistry<>ccl.net Subject: Overlap integrals in Gaussian 03 Message-ID: <20031205102556.GA8336<>iveta.uochb.cas.cz> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.28i From: Daniel Svozil >uochb.cas.cz> X-Spam-Status: No, hits=-2.5 required=7.0 tests=USER_AGENT_MUTT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi All, I need to check the linear dependency/independency of some additional basis functions, how do I make Gaussian 03 to print the values of the overlap integrals? Or is there any more clever way how to do this? Thanks in advance Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry and Center for Complex Molecular Systems and Biomolecules http://www.molecular.cz/ Czech Republic phone: +420-2-20 183 263 From chemistry-request@ccl.net Fri Dec 5 09:07:05 2003 Received: from web15408.mail.cnb.yahoo.com (web15408.mail.cnb.yahoo.com [202.43.216.211]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hB5E6Uxp028918 for ; Fri, 5 Dec 2003 09:06:32 -0500 Message-ID: <20031205140628.916.qmail(at)web15408.mail.cnb.yahoo.com> Received: from [211.138.102.93] by web15408.mail.cnb.yahoo.com via HTTP; Fri, 05 Dec 2003 22:06:28 CST Date: Fri, 5 Dec 2003 22:06:28 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: bond length problems 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, The following is a MOPAC input file. This molecule have 29 bonds, however, in this input file, there are 27 bonds. Why? How could I get the other two bond length? Thank you very much for any comments and suggestions. Best wishes, Jinsong 1SCF MMOK GEO-OK PM3 C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 1.406876 1 0.000000 0 0.000000 0 1 0 0 C 1.405594 1 119.774185 1 0.000000 0 2 1 0 C 1.407272 1 120.328476 1 0.000000 1 3 2 1 C 1.410172 1 119.830139 1 0.000000 1 4 3 2 C 1.405472 1 120.251541 1 0.000000 1 1 2 3 S 1.768463 1 120.276016 1 182.026047 1 5 4 3 O 1.531235 1 109.192093 1 139.154877 1 7 5 4 O 1.529861 1 110.722061 1 14.208542 1 7 5 4 C 1.818893 1 106.368225 1 256.936493 1 7 5 4 C 1.513687 1 111.811386 1 61.586670 1 10 7 5 O 1.228638 1 125.018021 1 273.977646 1 11 10 7 O 1.353775 1 113.909622 1 94.768494 1 11 10 7 C 1.407578 1 125.199875 1 185.026520 1 13 11 10 C 1.547882 1 117.712677 1 207.225830 1 10 7 5 C 1.545242 1 119.770691 1 274.953323 1 10 7 5 H 1.090408 1 120.074936 1 179.999634 1 1 2 3 H 1.090805 1 120.073196 1 179.999634 1 2 1 6 H 1.090515 1 120.099411 1 180.000366 1 3 2 1 H 1.091629 1 118.478531 1 180.000366 1 4 3 2 H 1.091141 1 118.578200 1 179.451462 1 6 1 2 H 1.115540 1 106.284302 1 177.258804 1 14 13 11 H 1.115356 1 112.264267 1 58.596680 1 14 13 11 H 1.115967 1 112.007233 1 295.757324 1 14 13 11 H 1.097015 1 119.490936 1 359.452713 1 15 10 7 H 1.097336 1 118.718079 1 219.862442 1 15 10 7 H 1.097580 1 118.394608 1 143.255173 1 16 10 7 H 1.096558 1 119.737473 1 3.705139 1 16 10 7 ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong(at)yahoo.com.cn __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Fri Dec 5 12:27:43 2003 Received: from hubble.deepsea.com (ip67-89-181-114.z181-89-67.customer.algx.net [67.89.181.114]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB5HRCxp001893 for ; Fri, 5 Dec 2003 12:27:12 -0500 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3BB55.045ED3B0" X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Subject: RE: Subject: young's modulus of air Date: Fri, 5 Dec 2003 09:27:11 -0800 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Subject: young's modulus of air Thread-Index: AcO7QkGoeltexA13QkK8t5Kw6FukbgAEiv5Q From: "Ray Merewether" To: "Akhalq.Ahmad" , X-Spam-Status: No, hits=1.9 required=7.0 tests=HTML_20_30,HTML_FONT_COLOR_BLUE,HTML_MESSAGE,HTML_WEB_BUGS, MAILTO_TO_SPAM_ADDR version=2.55 X-Spam-Level: * 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_001_01C3BB55.045ED3B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Young's modulus applies to solids (and some non-Newtonian liquids). You probably want a bulk modulus. You need to decide whether adiabatic = or isothermal will work for your application. If neither of those = extremes works, you'll need an equation of state for air. -----Original Message----- From: Akhalq.Ahmad [mailto:akhlaq95^at^kjist.ac.kr] Sent: Thursday, December 04, 2003 10:40 PM To: chemistry^at^ccl.net Subject: CCL:Subject: young's modulus of air Importance: Low I want to know th eyoung's modulus of elasticity of Air Regards Akhlaq, Ahmad MEMS&NanoPhotonics lab=20 Mechatronics Deptt. KwangJu Institute of Science & Technology=20 1 Oryong-Dong Buk-Gu Gwangju 500-712 Korea Cell. +82-18-875-1417=20 Res.# +82-62-970-2777 Off.# +82-62-970-2424=20 FAX # +82-62-970-2384=20 Homepage:-http://mems.kjist.ac.kr=20 E-mail:- akhlaq95^at^kjist.ac.kr = =20 -=3D This is automatically added to each message by the mailing script = =3D- 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=20 HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs=20 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) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ ------_=_NextPart_001_01C3BB55.045ED3B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Young's modulus applies to solids (and some=20 non-Newtonian liquids).

You=20 probably want a bulk modulus. You need to decide whether adiabatic = or=20 isothermal will work for your application. If neither of those = extremes=20 works, you'll need an equation of state for air.

-----Original Message-----
From: Akhalq.Ahmad=20 [mailto:akhlaq95^at^kjist.ac.kr]
Sent: Thursday, December 04, = 2003=20 10:40 PM
To: chemistry^at^ccl.net
Subject: = CCL:Subject:=20 young's modulus of air
Importance: Low

I = want to=20 know th eyoung's modulus of elasticity of=20 Air

Regards
Akhlaq, Ahmad
MEMS&NanoPhotonics = lab=20
Mechatronics Deptt. KwangJu Institute of Science & Technology =
1=20 Oryong-Dong Buk-Gu Gwangju 500-712 Korea
Cell. +82-18-875-1417 =
Res.#=20 +82-62-970-2777
Off.# +82-62-970-2424
FAX # +82-62-970-2384=20
Homepage:-http://mems.kjist.ac.kr
E-mail:- = akhlaq95^at^kjist.ac.kr
-=3D This is automatically added to each = message by the mailing script =3D- 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=20 HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs=20 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) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

------_=_NextPart_001_01C3BB55.045ED3B0-- From chemistry-request@ccl.net Fri Dec 5 11:19:16 2003 Received: from usstp06.itcs.purdue.edu (usstp06.itcs.purdue.edu [128.210.5.245]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB5GIjxp032439 for ; Fri, 5 Dec 2003 11:18:45 -0500 Received: from purdue.edu (chme117bpc3.ecn.purdue.edu [128.46.108.125]) by usstp06.itcs.purdue.edu (8.12.10/8.12.10/scan-smtp) with ESMTP id hB5GIjlv008930 for ; Fri, 5 Dec 2003 11:18:45 -0500 Message-ID: <3FD0AFE5.4000101^at^purdue.edu> Date: Fri, 05 Dec 2003 11:18:45 -0500 From: Aaron Deskins User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 CC: "CCL computational chemistry list (E-mail)" Subject: Cerium availability References: <9DD56492790889439F731F5BD6DACA0047FC74^at^srvkyem1.unitedcatalysts.com> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new on Purdue Mailhub X-Spam-Status: No, hits=-0.1 required=7.0 tests=MISSING_HEADERS,REFERENCES,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 fellow CCL-ers, I'm getting started on some surface calculations of CeO2, but am having trouble finding programs that support Ce. I imagine the problem is that you must have valence f orbitals. Gaussian has the CEP basis sets, so if worst comes to worst, I can set up a cluster model with Gaussian. Does anyone know of any programs (preferably periodic) that support Ce? Thank you for any help. Aaron Deskins Graduate Student Purdue University Chemical Engineering From chemistry-request@ccl.net Fri Dec 5 13:01:06 2003 Received: from med-gwia-01a.med.umich.edu (med-gwia-01a.med.umich.edu [141.214.93.149]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB5I0Yxp002772 for ; Fri, 5 Dec 2003 13:00:35 -0500 Received: from gwia-01-MTA by med-gwia-01a.med.umich.edu with Novell_GroupWise; Fri, 05 Dec 2003 13:00:34 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Beta Date: Fri, 05 Dec 2003 13:00:18 -0500 From: "Renxiao Wang" To: Subject: X-Score version 1.2 is available now Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline 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 CCLers, We would like to announce the release of X-Score version 1.2. X-Score is an empirical scoring function developed for protein-ligand binding affinity computation. Since its original release in late 2002, we have registered several hundreds of users all over the world. Compared to its previous version, X-Score version 1.2 has substantial improvements in many aspects: 1. All of the three scoring functions implemented in X-Score have been re-calibrated using a large set of 800 protein-ligand complexes. Thus, they will give more robust results for a wider range of biomolecular systems. 2. Users now have greater controls on the scoring functions used in computation. They are allowed to adjust the coefficient of each term to emphasize or underscore certain type of interactions between the protein and the ligand molecules. 3. More detailed outputs are available, which tabulate the role of each atom in binding score computation. This information helps users to analyze structure-affinity relationship in a more transparent way. 4. New utilities have been added to aid users to prepare the input structures more conveniently and more accurately. 5. Some bugs found in the previous version have been fixed. Many parts of the program have been optimized to give better performance. 6. User manual has been largely rewritten to reflect the many changes in version 1.2. New examples have been provided in the X-Score package for users to practice with this program. The X-Score v1.2 package can be downloaded for free from http://sw16.im.med.umich.edu/software/xtool/. New users are required to go through a registration procedure. Current users of X-Score may log on our server and dowload the program by following the instructions we sent to you before. Sincerely yours, Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine University of Michigan Medical School renxiao|at|med.umich.edu From chemistry-request@ccl.net Fri Dec 5 14:54:06 2003 Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB5JrXxp005805 for ; Fri, 5 Dec 2003 14:53:34 -0500 Received: from copland.udel.edu (localhost [127.0.0.1]) by copland.udel.edu (8.12.10/8.12.10) with ESMTP id hB5JrXLP021461 for ; Fri, 5 Dec 2003 14:53:33 -0500 (EST) Received: from localhost (odmitr@localhost) by copland.udel.edu (8.12.10/8.12.10/Submit) with ESMTP id hB5JrXdm021456 for ; Fri, 5 Dec 2003 14:53:33 -0500 (EST) Date: Fri, 5 Dec 2003 14:53:33 -0500 (EST) From: Olga G Dmytrenko To: chemistry[at]ccl.net Subject: Re:Solvated TS Searches Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Score: 0.3 DEAR_SOMEBODY,SPAM_PHRASE_00_01,USER_AGENT_PINE X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Dr. Hultin, I think we've had similar problems when did our studies on epoxidation reactions. A Computational Study Of The Hydroxyl-Group Directivity In The Peroxyformic Acid Epoxidation Of The Chiral Allylic Alcohol (Z)-3-Methyl-3-Penten-2-ol: Control Of Threo Diastereoselectivity Through Allylic Strain And Hydrogen Bonding, Adam, W.; Bach, R.D.; Dmitrenko, O.; Saha-Moeller C.R. J.OrgChem 65(20) (2000) 6715-6728 And scipcm model was the best at that time. Then we found that COSMO does great job and switched to it completely. From my experience, I can tell that one can do very different TSes optimizations at DFT+COSMO without much problems. But usually it's better to start from the gas phase TS, maybe correct the geometry in accord to the solvent-induced change of the reaction endo- or exothermicity (solvent can make TS either earlier or later, or do not affect at all). So, some chemical intuition is of great help. Usually if optimization in solvent is terminated abnormally, the increase of TSNUM helps. We do COSMO in gaussian98. As I see from the Andreas Klamt msg (THANKS!), it should be great in g03 and in GAMESS programs as well. Best regards, Olga From chemistry-request@ccl.net Fri Dec 5 15:06:57 2003 Received: from f04n01.cac.psu.edu (f04s01.cac.psu.edu [128.118.141.31]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB5K6Pxp006222 for ; Fri, 5 Dec 2003 15:06:25 -0500 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n01.cac.psu.edu (8.9.3p2.1/8.9.3) with ESMTP id PAA116808 for ; Fri, 5 Dec 2003 15:06:24 -0500 Subject: interpreting mulliken population analysis output From: Rajarshi Guha Reply-To: rxg218.-at-.psu.edu To: chemistry.-at-.ccl.net Content-Type: text/plain Organization: Message-Id: <1070654932.6681.12.camel.-at-.ra.chem.psu.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.2 (1.2.2-5) Date: 05 Dec 2003 15:08:53 -0500 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.3 required=7.0 tests=FROM_ENDS_IN_NUMS,MAILTO_TO_SPAM_ADDR,USER_AGENT_XIMIAN version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I'm trying to evaluate condensed Fukui indices using a mulliken population analysis (using the mullik option in Mopac 7.01). I have been referring to the Mendez et al, JACS, 1994, 116, 9298-9301 and they mention that to calculate, say f^{+}_{Ak} I need the charge of the kth atom in molecule A which they mention may be obtained by a Mulliken gross population analysis. The Mopac output has two sections: MULLIKEN POPULATION ANALYSIS and NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS. I'm not sure which section I should take the values for the charges from. If its the latter then extraction is not difficult. However if I need to use the former section I'm not sure as to how I should interpret the output. Would anybody have any pointers as to how I could interpret the MULLIKEN POPULATION ANALYSIS section of a Mopac run? Thanks, ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Every little picofarad has a nanohenry all its own. -- Don Vonada From chemistry-request@ccl.net Fri Dec 5 18:21:59 2003 Received: from mercury.chem.northwestern.edu (mercury.chem.northwestern.edu [129.105.116.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB5NLRxp011784 for ; Fri, 5 Dec 2003 18:21:27 -0500 Received: from mercury.chem.northwestern.edu (gayathri@localhost [127.0.0.1]) by mercury.chem.northwestern.edu (8.12.10/8.12.10) with ESMTP id hB5NLRNJ016098 for ; Fri, 5 Dec 2003 17:21:27 -0600 (CST) Received: from localhost (gayathri@localhost) by mercury.chem.northwestern.edu (8.12.10/8.12.10/Submit) with ESMTP id hB5NLQgb016095 for ; Fri, 5 Dec 2003 17:21:26 -0600 (CST) X-Authentication-Warning: mercury.chem.northwestern.edu: gayathri owned process doing -bs Date: Fri, 5 Dec 2003 17:21:25 -0600 (CST) From: Gayathri Narayanan To: Subject: Parallelization of force-routine Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.4 required=7.0 tests=USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi all, I need help regarding parallelization of force-routines. If anyone has parallelized a force-routine involving an atom-atom interaction potential for a condensed-phase system, using MPI or OpenMP commands, can you please let me know your suggestions/references? Thanks, Gayathri From chemistry-request@ccl.net Fri Dec 5 20:55:23 2003 Received: from yakko.cimav.edu.mx (yakko.cimav.ecustomer.mx [148.223.46.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB61spxp020631 for ; Fri, 5 Dec 2003 20:54:51 -0500 Received: from yakko (localhost [127.0.0.1]) by localhost.cimav.edu.mx (Postfix) with ESMTP id 38CBD1B8013 for ; Fri, 5 Dec 2003 18:54:39 -0700 (MST) Received: from localhost ([127.0.0.1]) by yakko.cimav.edu.mx (MailMonitor for SMTP v1.2.2 ) ; Fri, 5 Dec 2003 18:53:44 -0700 (MST) Received: from laquicom (dup-148-221-58-9.prodigy.net.mx [148.221.58.9]) by yakko.cimav.edu.mx (Postfix) with SMTP id 3431F1B8012 for ; Fri, 5 Dec 2003 18:53:43 -0700 (MST) Message-ID: <012901c3bb9b$d66a6dd0$093add94@laquicom> From: "Dr. Daniel Glossman-Mitnik" To: Subject: help for a talk Date: Fri, 5 Dec 2003 18:54:07 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0126_01C3BB61.29623670" 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-Spam-Status: No, hits=1.5 required=7.0 tests=HTML_50_60,HTML_MESSAGE,RCVD_IN_NJABL version=2.55 X-Spam-Level: * 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_0126_01C3BB61.29623670 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: I have been asked to give a talk on the relationship of computational chemistry with nanotechnology and of both with molecular medicine.=20 I will be grateful for some pointers to this subject. Thanks in advance Dr. Daniel Glossman-Mitnik ------=_NextPart_000_0126_01C3BB61.29623670 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear netters:

I have been asked to give a talk on the = relationship of

computational chemistry with = nanotechnology and of=20 both

with molecular medicine.

I will be grateful for some pointers to = this=20 subject.

Thanks in advance

&nbs= p; = ; =20 Dr. Daniel Glossman-Mitnik

------=_NextPart_000_0126_01C3BB61.29623670-- From chemistry-request@ccl.net Fri Dec 5 22:43:58 2003 Received: from front2.chartermi.net (front2.chartermi.net [24.213.60.124]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hB63hRxp023752 for ; Fri, 5 Dec 2003 22:43:27 -0500 Received: from [24.236.135.230] (HELO mmserver) by front2.chartermi.net (CommuniGate Pro SMTP 4.0.6) with SMTP id 250366728 for chemistry..at..ccl.net; Fri, 05 Dec 2003 22:43:23 -0500 Message-ID: <001401c3bbab$185ac730$0901a8c0@mmserver> From: "Jim Kress" To: References: <012901c3bb9b$d66a6dd0$093add94@laquicom> Subject: Re: CCL:help for a talk Date: Fri, 5 Dec 2003 22:43:21 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C3BB81.2F353FA0" 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-Spam-Status: No, hits=0.7 required=7.0 tests=HTML_40_50,HTML_MESSAGE,REFERENCES 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_0011_01C3BB81.2F353FA0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I've noticed lately that a number of CCL participants have requested = assistance in preparing presentations. Would it be possible to have the = finished versions of the presentations (prepared with CCL colleague = assistance) placed in the CCL archives for future CCL community use? That would seem a minimal repayment for the assistance provide by the = CCL community. Jim ----- Original Message -----=20 From: Dr. Daniel Glossman-Mitnik=20 To: chemistry..at..ccl.net=20 Sent: Friday, December 05, 2003 8:54 PM Subject: CCL:help for a talk Dear netters: I have been asked to give a talk on the relationship of computational chemistry with nanotechnology and of both with molecular medicine.=20 I will be grateful for some pointers to this subject. Thanks in advance Dr. Daniel Glossman-Mitnik ------=_NextPart_000_0011_01C3BB81.2F353FA0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

I've noticed lately that a number of = CCL=20 participants have requested assistance in preparing presentations. = Would=20 it be possible to have the finished versions of the presentations = (prepared with=20 CCL colleague assistance) placed in the CCL archives for future CCL = community=20 use?

That would seem a minimal repayment for = the=20 assistance provide by the CCL community.

Jim

----- Original Message -----
From:=20 Dr. Daniel = Glossman-Mitnik=20
To: chemistry..at..ccl.net

Sent: Friday, December 05, 2003 = 8:54=20 PM

Subject: CCL:help for a = talk

Dear netters:

I have been asked to give a talk on = the=20 relationship of

computational chemistry with = nanotechnology and=20 of both

with molecular medicine. =

I will be grateful for some pointers = to this=20 subject.

Thanks in advance

&nbs= p; = ; =20 Dr. Daniel Glossman-Mitnik

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