From wall@phys.chem.ethz.ch Tue Jul 21 01:51:59 1998 Received: from phys.chem.ethz.ch (helios-chem.ethz.ch [129.132.102.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA12858 Tue, 21 Jul 1998 01:51:58 -0400 (EDT) Received: from bacon.ethz.ch (bacon.ethz.ch [129.132.44.28]) by phys.chem.ethz.ch (8.8.8/8.8.8) with SMTP id HAA20499; Tue, 21 Jul 1998 07:51:55 +0200 (MET DST) Date: Tue, 21 Jul 1998 07:51:59 +0200 (CEST) From: Ernst-Udo Wallenborn To: Davide Proserpio cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:G:Gaussian expansion of Slater-type orbitals In-Reply-To: <199807201514.RAA09298@stinch10.csmtbo.mi.cnr.it> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 20 Jul 1998, Davide Proserpio wrote: >I am looking for a program that can input simple or double >zeta slater type orbitals (the one used in extended Huckel calculations) >and give be the best gaussian expansion (4, 6 or more functions). You may wish to have a look at Lopez et al, J. Chim. Phys. _84_ 695 (1987) Rico et al, Collect. Czech. Chem. Comm. _53_ 2250 (1987) V.R. Saunders. Computational Techniques in Quantum Chemistry and Molecular Physics, G.H.F. Diercksen, B.T. Sutcliffe and A. Veillard, Eds. (D. Reidel, Boston, 1975) 347-392. Rico et al, Comp. Phys. Comm. _105_ 216 (1997) -- Ernst-Udo Wallenborn Laboratorium fuer Physikalische Chemie ETH Zuerich From jochen@uni-duesseldorf.de Tue Jul 21 03:25:34 1998 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA13432 Tue, 21 Jul 1998 03:25:33 -0400 (EDT) Received: from bacchus (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id JAA12080; Tue, 21 Jul 1998 09:25:13 +0200 From: Jochen Kuepper Reply-To: jochen@uni-duesseldorf.de To: "Kynn O. Jones" Subject: Re: CCL:RCS in scientific programming Date: Thu, 14 May 48409 07:58:41 +0200 X-Mailer: KMail [version 0.7.9] Content-Type: text/plain Cc: CCL References: <199807202201.SAA21007@panix3.panix.com> MIME-Version: 1.0 Message-Id: <98072109251200.11036@bacchus> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id DAA13432 On Tue, 21 Jul 1998 Kynn O. Jones wrote: >For my research, I typically have several versions of any my code that >I work with concurrently. (Each version, of course, perforsm a >different task). The source files for these versions differ from each >other in relatively minor ways, but yet substantially enough that it >would be too confusing to merge them all into a single source and use >preprocessor switches to differentiate among the various versions. > >Needless to say, it quickly becomes difficult to keep track of all >these similar source files. I have heard repeatedly, both from >scientific and "non-scientific" programmers that RCS is *the* tool to >take care of this situation, but hard as I've tried, I've never [snip] Well, I would say RCS is not _the_ tool to use. You should sreiously look at CVS at www.cyclic.com. That is like RCS for a full source repository instead of single files. It will still have most of the problems you described in you message, but anyhow, why don't you split your programs into common and distinguished parts anyhow ? Think about your projects design once more, porbably ? If you can change that, you might go an much easier way than hacking rcs or cvs. Greetings, Jochen ----------------------------------------------------------------------- Jochen K"upper Heinrich-Heine-Universit"at D"usseldorf jochen@uni-duesseldorf.de Institut f"ur Physikalische Chemie I Universit"atsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 D"usseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From boufer@cennas.nhmfl.gov Tue Jul 21 08:18:12 1998 Received: from cennas.nhmfl.gov (cennas.nhmfl.gov [146.201.220.8]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA14703 Tue, 21 Jul 1998 08:18:11 -0400 (EDT) Received: from localhost (boufer@localhost) by cennas.nhmfl.gov (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id JAA12782; Tue, 21 Jul 1998 09:19:24 -0400 (EDT) Date: Tue, 21 Jul 1998 09:19:24 -0400 (EDT) From: Ahmed Bouferguene To: g-d@CCMSD.chem.uga.edu cc: chemistry@www.ccl.net Subject: Derivatives of the Density matrix / nuclear coordinates In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings all, Does anybody know where the derivatives of the density matrix with respect to nuclear X,Y,Z are stored in G-92 or G-94. Actually I have been wandering in l1002.F without any success. All I managed to get was the derivatives with respect to the electric field. Thanks for your time and Help. From tp@elptrs7.rug.ac.be Tue Jul 21 12:50:04 1998 Received: from elptrs7.rug.ac.be (elptrs7.rug.ac.be [157.193.112.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA22994 Tue, 21 Jul 1998 12:50:01 -0400 (EDT) Received: from localhost by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA16232; Tue, 21 Jul 1998 18:49:44 +0200 Date: Tue, 21 Jul 1998 18:49:43 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List Subject: PC video conference installation (off-topic) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, Excuse me for my asking this off topic question. I'm willing to install a video conference system using a PC and a modem, which will be used for video communications between Europe and US. Can anybody inform me what I should prepare for that? What I guess now is that I need a good PC with sound card, graphic card, digital camera, and a fast modem. But what else do I need in the hardware side? What softwares are needed and how can I make the connection for the PC video conference? Any information would be greatly appreciated. Thanks in advance. tp From hinsen@dirac.cnrs-orleans.fr Tue Jul 21 13:44:05 1998 Received: from dirac.cnrs-orleans.fr (dirac.cnrs-orleans.fr [163.9.6.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA26487 Tue, 21 Jul 1998 13:44:03 -0400 (EDT) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.7/8.7) id TAA20146; Tue, 21 Jul 1998 19:43:36 +0200 (DFT) Date: Tue, 21 Jul 1998 19:43:36 +0200 (DFT) Message-Id: <199807211743.TAA20146@dirac.cnrs-orleans.fr> From: Konrad Hinsen To: MARYJO@NEU.EDU CC: chemistry@www.ccl.net In-reply-to: <01IZIMYEDJOYADG67P@neu.edu> (MARYJO@NEU.EDU) Subject: Re: CCL:gradients References: <01IZIMYEDJOYADG67P@neu.edu> > I have a 3-D space and can calculate the value of the function > at any sets of points in the space that I choose. I must > calculate the gradient of my function. Can anybody give me > some pointers about the best way to do this (both in terms of > comnputational efficiency and accuracy)? Is it best to take It all depends on your needs. Here are the options: - Finite differences. This requires nothing but the possibility to calculate your function at any point, but it is an approximation. You can then either calculate your function at every point on a rectangular grid, and then take the derivatives all over the grid, or you can evaluate the function around a given point as needed. For an implementation of the first approach, for rectangular but not necessarily equidistant grids, see http://starship.skyport.net/crew/hinsen/Interpolation.py (that's in Python). - Analytic derivatives. That gives the best accuracy and usually also efficiency, but it requires you to know the functional form of your function analytically. If you are distracted by the hard work of calculating derivatives, computer algebra packages like Mathematica or Maple could be of use. - Automatic derivatives. That's an intermediate strategy, which calculates the analytic derivative numerically by applying the chain rule implicitly. It works for all functions that can be written in terms of a set of elementary functions whose derivatives are known analytically. For an implementation, see http://starship.skyport.net/crew/hinsen/Derivatives.py (that's in Python as well). -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From dgao@chem.iupui.edu Tue Jul 21 14:02:27 1998 Received: from hydroxyl.chem.iupui.edu (hydroxyl.chem.iupui.edu [134.68.136.154]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id OAA27270 Tue, 21 Jul 1998 14:02:27 -0400 (EDT) Received: from localhost by hydroxyl.chem.iupui.edu (950413.SGI.8.6.12/MSU-2.04) id RAA04834; Tue, 21 Jul 1998 17:51:03 GMT Date: Tue, 21 Jul 1998 12:51:03 -0500 (EST) From: Daquan Gao To: "Park, Tae-Yun" cc: Computational Chemistry List Subject: Re: CCL:PC video conference installation (off-topic) In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I think I have all the things you mentioned on my PC. I have not got that to work though, probably because the other side of my "conference" is having problems. daquan On Tue, 21 Jul 1998, Park, Tae-Yun wrote: > Hi all, > > Excuse me for my asking this off topic question. I'm willing to > install a video conference system using a PC and a modem, which will > be used for video communications between Europe and US. > > Can anybody inform me what I should prepare for that? What I guess now > is that I need a good PC with sound card, graphic card, digital camera, > and a fast modem. But what else do I need in the hardware side? What > softwares are needed and how can I make the connection for the PC video > conference? > > Any information would be greatly appreciated. > > Thanks in advance. > > tp > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: tp@elptrs7.rug.ac.be > -- Original Sender From: Address: tp@elptrs7.rug.ac.be > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From Krys.Radacki@ac.rwth-aachen.de Tue Jul 21 16:19:45 1998 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA29010 Tue, 21 Jul 1998 16:19:44 -0400 (EDT) Received: from Zosia (zosia.dorf.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-10 #30440) with SMTP id <01IZOFJXUIKQ0005CH@mail.rwth-aachen.de> for CHEMISTRY@www.ccl.net; Tue, 21 Jul 1998 22:20:59 +0200 Date: Tue, 21 Jul 1998 22:19:43 +0200 From: Krzysztof Radacki Subject: Re: x,y,z vs. internal coordinates In-reply-to: <199807170531.OAA23155@deews1.dent.okayama-u.ac.jp> X-Sender: kradacki@mail.rwth-aachen.de To: CHEMISTRY@www.ccl.net Message-id: <3.0.3.32.19980721221943.006a9628@mail.rwth-aachen.de> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Content-type: text/plain; charset="us-ascii" At 02:48 PM 17.07.1998 +0900, you wrote: >Dear Sir: > > I ask about the following. > >(1) The optimization using x,y,z coordinates is faster than that using >internal coordinates. > >(2) Do you experience that the optimization using x,y,z coordinates >converges unexpected optimized structure ? The optimization using >internal coordinates is more safe than the optimization using x,y,z >coordinates ? > I would say in both question contrary. Imternal coordinates are faster (useing symmetry and reduced amounts of variable like all 3 bonds on Me) but not always stable (good exp. if in Gaussian you will have angle near 0 or 180 degree). regards Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ---------------------------------------------------------------------------- - From adam@cherwell.com Thu Jul 16 07:34:16 1998 Received: from congo.cherwell.com (congo.cherwell.com [193.82.249.202]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA05307 Thu, 16 Jul 1998 07:34:13 -0400 (EDT) Received: from wharfe.cherwell.com ([193.82.249.214]) by congo.cherwell.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-0U10L2S100) with SMTP id AAA387; Thu, 16 Jul 1998 12:34:03 +0100 Message-Id: <3.0.5.32.19980716123353.0080d2a0@cherwell.com> X-Sender: adam@cherwell.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Thu, 16 Jul 1998 12:33:53 +0100 To: chemistry@www.ccl.net From: Adam Hodgkin Subject: Training in ChemSymphony and JavaBeans Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues We announce two one-day training courses for JavaBeans in Chemistry which we will be holding in Oxford on August 6 and August 7, 1998. The first course 'Developing Intranets with ChemSymphony Beans' (August 6) is introductory and is aimed at IS managers or Computational Chemists who need a rapid overview of the JavaBeans technology for chemistry. The second course 'Java programming with ChemSymphony Beans' (August 7) and is designed for programmers who have some basic knowledge of Java. Visit our www site for details, map, registration form etc: http://www.chemsymphony.com/Beans/training.html Best wishes Adam --- --- Adam Hodgkin | e-mail: adam@cherwell.com Chairman | Phone: +44 (0)1865 784810 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford OX4 4GA, UK | URL: http://www.cherwell.com --- --- From dgao@chem.iupui.edu Fri Jul 17 10:33:22 1998 Received: from hydroxyl.chem.iupui.edu (hydroxyl.chem.iupui.edu [134.68.136.154]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA15812 Fri, 17 Jul 1998 10:33:21 -0400 (EDT) Received: from localhost by hydroxyl.chem.iupui.edu (950413.SGI.8.6.12/MSU-2.04) id OAA26908; Fri, 17 Jul 1998 14:22:50 GMT Date: Fri, 17 Jul 1998 09:22:49 -0500 (EST) From: Daquan Gao To: "Hui-Hsu (Gavin) Tsai" cc: chemistry@www.ccl.net Subject: Re: CCL:delicate workstation for ab initio calculations In-Reply-To: <199807170205.WAA24258@babar.INS.CWRU.Edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Just one comment, it seems you have got more than enough money for "one" work station. Daquan On Thu, 16 Jul 1998, Hui-Hsu (Gavin) Tsai wrote: > Dear Computational Chemists: > > We consider to buy one delicate workstation to perform > ab initio calculations (Becke3LYP/6-31G** level with geometry optimization > and vibration calculations) of metalloporphyrins (at least 45 heavy atoms). > > I do not know what kind of workstations is excellent to do these > calculations now because the computer techniques progress very fast. > Has anyone comments or suggestions in purchasing the workstation to perform > these large-scale calculations. > Our budget is about $60000.00. Any comment, experience, and suggestion is > welcomed. > > Thanks a lot. > > Gavin Tsai > Case Western Reserve University > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: hxt10@po.cwru.edu > -- Original Sender From: Address: hxt10@po.cwru.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From lavelle@mbi.ucla.edu Sat Jul 18 14:43:47 1998 Received: from theta1.ben2.ucla.edu (theta1.ben2.ucla.edu [164.67.131.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA23780 Sat, 18 Jul 1998 14:43:47 -0400 (EDT) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by theta1.ben2.ucla.edu (8.8.8/8.8.8) with SMTP id LAA15270; Sat, 18 Jul 1998 11:43:49 -0700 Received: from pc-ll.chem.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA25267; Sat, 18 Jul 1998 11:43:48 -0700 Message-Id: <9807181843.AA25267@ewald.mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0 Date: Sat, 18 Jul 1998 11:56:31 -0700 To: "C.F. Matta" , Yongxing Liu From: Laurence Lavelle Subject: Re: CCL:Re: CCL:Experimental solvation free energy results for biomacromolecules Cc: chemistry@www.ccl.net In-Reply-To: References: <199807102105.RAA28990@mail.wesleyan.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Is there anything on solvation free energies of nucleic acids? Laurence At 01:04 AM 7/15/98 -0400, C.F. Matta wrote: > > > >Dear Yongxing, > > Experimental free energies of transfer of the amino acids side-chains >from the vapor phase to aqueous phase (pH 7) can be found in: >R. Wolfenden, L. Andersson, P. M. Cullis, and C. C. B. Southgate >"Affinities of Amino Acid Side Chains for Solvent Water", Biochemistry 20, >1981, pp.849-855. > > Take care. > > Cherif Matta > Graduate student > Chemistry Department > McMaster University > Hamilton, Ontario > Canada L8S 4M1 > >On Fri, 10 Jul 1998, Yongxing Liu wrote: > >> >> Dear Friends, >> >> I would like to know if there is some information about experimental >> solvation free energy results for biomacromolecules(peptides, proteins, DNAs >> and RNAs). Please e-mail any resources from which I can get the related data. >> >> Thanks a lot in advance >> >> -------------------------------------------------------------------------- >> Yongxing Liu, Graduate Student | E-Mail: yliu@wesleyan.edu >> Department of Chemistry | Tel.:860-685-2777 >> Wesleyan University | Fax: 860-685-2211 >> Middletown CT 06459 | URL: http://ludwig.chem.wesleyan.edu/yliu >> >> --------------------------------------------------------------------------- >> >> >> >> --- >> Administrivia: This message is automatically appended by the mail exploder: >> CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >> MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >> Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search >> Web: http://www.ccl.net/chemistry.html >> --- >> >> > > > >--- >Administrivia: This message is automatically appended by the mail exploder: >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html >--- > From ccl@www.ccl.net Mon Jul 20 11:11:40 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA00601 Mon, 20 Jul 1998 11:11:40 -0400 (EDT) Received: from ck-sg.p.lodz.pl (ck-sg.p.lodz.pl [193.59.44.78]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA18506; Mon, 20 Jul 1998 11:10:50 -0400 (EDT) Received: (from paneth@localhost) by ck-sg.p.lodz.pl (980427.SGI.8.8.8/970903.SGI.AUTOCF) id RAA09471; Mon, 20 Jul 1998 17:07:58 +0200 (MDT) Date: Mon, 20 Jul 1998 17:07:58 +0200 (MDT) From: Piotr Paneth To: chemistry@ccl.net cc: Takanobu Ishida , Ostlund Neil S , William Saunders , Andy Holder , Bogdan Lesyng , Jeffrey A Smiley , Debra Dunaway-Mariano , Jerzy Rudzinski , Joseph J Gajewski , W Andrzej Sokalski , Vern Schramm , John Marlier , Paul Cook , W Cleland , Frank Jensen , Todd Swanson , Mirek Sopek , Donald G Truhlar , Christopher J Cramer , "Marion O'Leary" , Paul Berti , Mike Schmidt , Ruma Banerjee , Anisimov V , Olle Matsson , KWESTAWA@NICKEL.LAURENTIAN.CA, Alvan Hengge , Vernon Anderson , David Berkowitz , Thomas Bally , Jerzy Ciarkowski , Jan Labanowski , Etienne Roth , Jacob Bigeleisen , Max Wolfsberg , blanchar@aecom.yu.edu, tcbruice@bioorganic.ucsb.edu, call@aecom.yu.edu, epstein@gps.caltech.edu, fitzpat@bioch.tamu.edu, horen@chem.ufl.edu, huskey@andromeda.Rutgers.EDU, zafral@aol.com, limbach@chemie.fu-berlin.de, daniel-quinn@uiowa.edu, ms@gaus90.chem.yale.edu, shiner@indiana.edu, vanhook@novell.chem.utk.edu, warshel@invitro.usc.edu Subject: ISOEFF98 announcement Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A new release of our program for calculations of isotope effects from quantum-chemical results is now available at: http://ck-sg/isoeff/isoeff.html The major improvement over previous versions is the addition of routines which allow the user to change force constants for selected internal coordinates and to see the effect of these changes on the calculated isotope effects (like in the BEBOVIB but at the quantum-chemical level). ******************************************************************************** Prof. Dr. Hab. Piotr Paneth Department of Chemistry (I-19) phone: (+48-42) 631-3199 Technical University of Lodz fax: (+48-42) 636-5008 Zeromskiego 116, 90-924 Lodz, Poland E-mail: paneth@ck-sg.p.lodz.pl From wagenert@mailer.uni-marburg.de Mon Jul 20 11:16:21 1998 Received: from Mailer.Uni-Marburg.DE (Mailer.Uni-Marburg.DE [137.248.1.71]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA00680 Mon, 20 Jul 1998 11:16:15 -0400 (EDT) Received: from palladium (pc15125.Chemie.Uni-Marburg.DE [137.248.151.10]) by Mailer.Uni-Marburg.DE (8.8.5/8.8.5) with ESMTP id RAA14484 for ; Mon, 20 Jul 1998 17:16:09 +0200 Message-ID: <000401bdb3f1$ad1533a0$0a97f889@palladium.chemie.uni-marburg.de> From: "Thomas Wagener" To: Subject: Postdoctoral position Date: Mon, 20 Jul 1998 17:18:35 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Hi everybody, I am forwarding this message for my boss. Please send *all replies* to **him**. The e-mail is given below. Cheers, Thomas Wagener ---------------------------------------------------------------------------- ------------------ Dear Collegues, I am looking for a candidate for a POSTDOCTORAL POSITION in my group. Research area: Quantum chemical studies of the reaction mechanismen of transition metal catalyzed processes. Requirements: Ph.D. in Theoretical/Computational Chemistry. Experience in the application of ab initio and/or DFT methods for the calculation of the structures and reaction pathways of molecules. Ability to communicate and to cooperate with experimentalists, because the project is part of a combined theoretical/experimental group project with the aim to find new catalysts. Ability to work indepently. Starting date: The position is open immediately. Duration: 2 years. Salary: BAT/IIa (Approximately DM 2800 - 3300 per month, after tax). The project is funded by the BMBF (german state secretary of science and education) The candidate should send his CV and arrange for three letters of recommendation to be send to my address below. I appreciate your help in finding a good candidate. Please feel free to forward this mail to anyone who might be interested in the position. Professor Gernot Frenking Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Strasse D-35032 Marburg Germany Tel.: (06421)285563 (06421)281535 (Secr.) FAX: (06421)282189 Email: frenking@ps1515.chemie.uni-marburg.de Website: www.chemie.uni-marburg.de/~frenking/ From ccl@www.ccl.net Mon Jul 20 11:41:01 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA01043 Mon, 20 Jul 1998 11:41:01 -0400 (EDT) Received: from ck-sg.p.lodz.pl (ck-sg.p.lodz.pl [193.59.44.78]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA19397; Mon, 20 Jul 1998 11:40:48 -0400 (EDT) Received: (from paneth@localhost) by ck-sg.p.lodz.pl (980427.SGI.8.8.8/970903.SGI.AUTOCF) id RAA12021; Mon, 20 Jul 1998 17:41:28 +0200 (MDT) Date: Mon, 20 Jul 1998 17:41:28 +0200 (MDT) From: Piotr Paneth To: chemistry@ccl.net cc: Takanobu Ishida , Ostlund Neil S , William Saunders , Andy Holder , Bogdan Lesyng , Jeffrey A Smiley , debra dunaway-mariano , Jerzy Rudzinski , Joseph J Gajewski , W Andrzej Sokalski , Vern Schramm , John Marlier , Paul Cook , W Cleland , Frank Jensen , Todd Swanson , Mirek Sopek , Donald G Truhlar , Christopher J Cramer , "Marion O'Leary" , Paul Berti , Mike Schmidt , Ruma Banerjee , Anisimov V , Olle Matsson , KWESTAWA@NICKEL.LAURENTIAN.CA, Alvan Hengge , Vernon Anderson , David Berkowitz , Thomas Bally , Jerzy Ciarkowski , Jan Labanowski , Etienne Roth , Jacob Bigeleisen , Max Wolfsberg , blanchar@aecom.yu.edu, tcbruice@bioorganic.ucsb.edu, call@aecom.yu.edu, epstein@gps.caltech.edu, fitzpat@bioch.tamu.edu, horen@chem.ufl.edu, huskey@andromeda.Rutgers.EDU, zafral@aol.com, limbach@chemie.fu-berlin.de, daniel-quinn@uiowa.edu, ms@gaus90.chem.yale.edu, shiner@indiana.edu, vanhook@novell.chem.utk.edu, warshel@invitro.usc.edu Subject: Isoeff98 http-correction Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sorry for misleading address. It is: http://ck-sg.p.lodz.pl/isoeff/isoeff.html ******************************************************************************** Prof. Dr. Hab. Piotr Paneth Department of Chemistry (I-19) phone: (+48-42) 631-3199 Technical University of Lodz fax: (+48-42) 636-5008 Zeromskiego 116, 90-924 Lodz, Poland E-mail: paneth@ck-sg.p.lodz.pl From ccl@www.ccl.net Mon Jul 20 18:01:29 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA11277 Mon, 20 Jul 1998 18:01:28 -0400 (EDT) Received: from ha1.rdc1.sfba.home.com (siteadm@ha1.rdc1.sfba.home.com [24.0.0.66]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id SAA01590 for ; Mon, 20 Jul 1998 18:01:20 -0400 (EDT) Received: from home.com ([24.1.88.89]) by ha1.rdc1.sfba.home.com (Netscape Mail Server v2.02) with ESMTP id AAA25319; Mon, 20 Jul 1998 15:01:18 -0700 Message-ID: <35B3BF70.B4E59F67@home.com> Date: Mon, 20 Jul 1998 15:06:40 -0700 From: John Dunbar Reply-To: savesoft@aol.com Organization: @Home Network X-Mailer: Mozilla 4.02 [en]C-AtHome0402 (Win95; U) MIME-Version: 1.0 To: pigdog-l@arlington.com CC: Chemistry@ccl.net Subject: Re: [Pigdog] CCL:Solid Rocket Fuel Emissions References: <27503-359CF9B6-106@mailtod-101.iap.bryant.webtv.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Berry, This is a loaded question because solid fuels come in a variety of forms and compositions. They also have different burn characteristics based upon the thermochemistry involved, the type of fuel, and shape of fuel grains. There is also the enthalpy to consider, sometimes called the Q reaction. Heat of fusion and vaporization must also be considered. You can attempt to predict the products of combustion with the Equilibrium Constant method, or with the Minimization of Free Energy method. Both of these examine the change in heat of reaction and use our friend PV = nrT. ( Note there are 3 equations a good physicist never forgets: PV = nrT, E = 1/2kt , and F = Gamma*ma + qE from these just about every useful equation known to mankind can be derived! ) So, it really does depend upon what are your reactants, how will they burn, i.e. pressure and geometry of burn, the binder in the propellant, and a little statistical analysis. I would love to discuss this offline with you. I am currently involved in hybrid engines ( N20 + fuel ). I'm also a HAM operator. My call sign is KE6WBO. I don't have a rig at the moment, but I do amature TV telemtry from rockets. I'm invlovled in a project to place a 12" hybrid about 200mi up, and downlink telemtry via video overlay. If you are serious, I would love to discuss fuel propulsion and reactions. Best bet contact me at blackfu2@aol.com. I'm using hanging out on AOL. Jonathan p.s. You may want to ask Thom Stark. He knows far more than anyone I have ever heard of studying rocket propulsion and propellant mixtures. BARRY BITTINGER SR. wrote: > > I respectfully request your input into my concerns about what chemicals > are emitted in the smoke of thermal chemical fuel, specifically solid > rocket fuel, when all these chemicals are burned together at one time? > atomized aluminm powder (fuel) 16% > ammonium perchlorate (oxidizer) 69.83% > iron oxide powder (catalyst) 17% (varies) > polybutadiene acrylic acid acrylonitrite (binder) 12% AKA > carbonated polyester > epoxy curing agent 2% > Thank you very much. I would appreciate feedback. > > From Barry W. Bittinger Sr. > > SCIENCELINK@webtv.net > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- From ccl@www.ccl.net Mon Jul 20 18:01:29 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA11277 Mon, 20 Jul 1998 18:01:28 -0400 (EDT) Received: from ha1.rdc1.sfba.home.com (siteadm@ha1.rdc1.sfba.home.com [24.0.0.66]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id SAA01590 for ; Mon, 20 Jul 1998 18:01:20 -0400 (EDT) Received: from home.com ([24.1.88.89]) by ha1.rdc1.sfba.home.com (Netscape Mail Server v2.02) with ESMTP id AAA25319; Mon, 20 Jul 1998 15:01:18 -0700 Message-ID: <35B3BF70.B4E59F67@home.com> Date: Mon, 20 Jul 1998 15:06:40 -0700 From: John Dunbar Reply-To: savesoft@aol.com Organization: @Home Network X-Mailer: Mozilla 4.02 [en]C-AtHome0402 (Win95; U) MIME-Version: 1.0 To: pigdog-l@arlington.com CC: Chemistry@ccl.net Subject: Re: [Pigdog] CCL:Solid Rocket Fuel Emissions References: <27503-359CF9B6-106@mailtod-101.iap.bryant.webtv.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Berry, This is a loaded question because solid fuels come in a variety of forms and compositions. They also have different burn characteristics based upon the thermochemistry involved, the type of fuel, and shape of fuel grains. There is also the enthalpy to consider, sometimes called the Q reaction. Heat of fusion and vaporization must also be considered. You can attempt to predict the products of combustion with the Equilibrium Constant method, or with the Minimization of Free Energy method. Both of these examine the change in heat of reaction and use our friend PV = nrT. ( Note there are 3 equations a good physicist never forgets: PV = nrT, E = 1/2kt , and F = Gamma*ma + qE from these just about every useful equation known to mankind can be derived! ) So, it really does depend upon what are your reactants, how will they burn, i.e. pressure and geometry of burn, the binder in the propellant, and a little statistical analysis. I would love to discuss this offline with you. I am currently involved in hybrid engines ( N20 + fuel ). I'm also a HAM operator. My call sign is KE6WBO. I don't have a rig at the moment, but I do amature TV telemtry from rockets. I'm invlovled in a project to place a 12" hybrid about 200mi up, and downlink telemtry via video overlay. If you are serious, I would love to discuss fuel propulsion and reactions. Best bet contact me at blackfu2@aol.com. I'm using hanging out on AOL. Jonathan p.s. You may want to ask Thom Stark. He knows far more than anyone I have ever heard of studying rocket propulsion and propellant mixtures. BARRY BITTINGER SR. wrote: > > I respectfully request your input into my concerns about what chemicals > are emitted in the smoke of thermal chemical fuel, specifically solid > rocket fuel, when all these chemicals are burned together at one time? > atomized aluminm powder (fuel) 16% > ammonium perchlorate (oxidizer) 69.83% > iron oxide powder (catalyst) 17% (varies) > polybutadiene acrylic acid acrylonitrite (binder) 12% AKA > carbonated polyester > epoxy curing agent 2% > Thank you very much. I would appreciate feedback. > > From Barry W. Bittinger Sr. > > SCIENCELINK@webtv.net > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- From bernhold@npac.syr.edu Mon Jul 20 21:06:22 1998 Received: from snake.npac.syr.edu (snake.npac.syr.edu [128.230.162.60]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA12113 Mon, 20 Jul 1998 21:06:22 -0400 (EDT) Received: from localhost (bernhold@localhost) by snake.npac.syr.edu (950413.SGI.8.6.12/8.6.6) with SMTP id VAA23925; Mon, 20 Jul 1998 21:06:16 -0400 Message-Id: <199807210106.VAA23925@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: Host localhost didn't use HELO protocol Reply-to: bernhold@npac.syr.edu To: ross@cgl.ucsf.edu cc: chemistry@www.ccl.net cc: bernhold@npac.syr.edu Subject: Re: CCL:RCS in scientific programming In-reply-to: <199807202345.QAA25426@socrates.cgl.ucsf.EDU> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <23922.900983176.1@snake.npac.syr.edu> Date: Mon, 20 Jul 1998 21:06:16 -0400 From: "David E. Bernholdt" On Mon, 20 Jul 1998 16:45:37 -0700 (PDT) ross@cgl.ucsf.edu wrote: > CVS may be the answer ... It may not handle the desired parallel > versions though. It doesn't. > At the very least, I'd encourage all linearly-oriented > RCS users to go to CVS. I agree with this -- I have been using CVS since the late 1980s and I think it is much superior to raw RCS, even if you're the only developer on the project. -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From ep7@dent.okayama-u.ac.jp Tue Jul 21 20:10:40 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA01154 Tue, 21 Jul 1998 20:10:37 -0400 (EDT) From: ep7@dent.okayama-u.ac.jp Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id JAA13768 for ; Wed, 22 Jul 1998 09:11:51 +0900 (JST) Message-Id: <199807220011.JAA13768@deews1.dent.okayama-u.ac.jp> Date: Wed, 22 Jul 1998 09:29:00 +0900 To: CHEMISTRY@www.ccl.net Subject: CCL:Summary: X,Yx,Z vs. internal coordinates MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Sir: I summarized x,y,z vs. internal coordinates. Masao Masamura Preventive Dentistry Okayama University Dental School Shikata-cho, 2-5-1 Okayama 700 Japan FAX: 81-86-235-6714 e-mail: ep7@dent.okayama-u.ac.jp I ask about the following. (1) The optimization using x,y,z coordinates is faster than that using internal coordinates. (2) Do you experience that the optimization using x,y,z coordinates converges unexpected optimized structure ? The optimization using internal coordinates is more safe than the optimization using x,y,z coordinates ? Thank you. > (1) The optimization using x,y,z coordinates is faster than that using > internal coordinates. No, generally not. Because in internal coord. you optimize 3N-6 variables, whereas in xyz you have 3N. > > (2) Do you experience that the optimization using x,y,z coordinates > converges unexpected optimized structure ? The optimization using > internal coordinates is more safe than the optimization using x,y,z > coordinates ? Yes and no. For cyclic systems or bigger molecules, a little deviation of one variable like an angle can cause big distortions of your molecule. For example, since C1 and C6 in a 6-membered ring are not "connected", changing the dihedral 2-3-4-5 by 50 causes a relativily great change in bond length for C1-C6. There are more types of coordinates like the redundant internal coordinates used in Gaussian. There is also a neverending debate about the "right" ones. See their manual at www.gaussian.com for references. -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- I would like to ask about the following. (1) The redundant internal coordinates is more reliable ? (2) What is www.gaussian.com ? (3) The optimization using the redundant internal coordinates is faster than the optimization using x,y,z coordinates ? > (1) The redundant internal coordinates is more reliable ? They say so. These coord. have the advantage of being redundant, i.e., there are achieved additional coord. from your input., so the system can change to other coord. during opt. > (2) What is www.gaussian.comwww.gaussian.com ? http://www.gaussian.com > (3) The optimization using the redundant internal coordinates is faster > than the optimization using x,y,z coordinates ? More likely leeding to convergence I would think > About the second item I have no experience, although it sounds a bit strange. However, for the first one, I can say that generally it is the opposite and optimization in the internal coordinates are much faster than cartesian coordinates. For some special cases, however, it is not straightforward to set up a suitable internal coordinate set which can be properly used during the optimization and one has to use the XYZ coordinates (or redundant internal coordinates, if implemented). I have heard arguments on both sides. One the one hand, optimization steps taken in torsion space are thought by many to follow more closely the natural low energy pathways in molecules, or at least in proteins. This argument seems to be backed up by recent numerical experiments in Ruben Abagyan's group: Abagyan R.A. and Totrov, M.M. J. Mol. Bio 235 (1994) 983 (which admittedly I have not read), in which they measure how far one can move away from a local minimum and still return via optimization. Others argue that by restricting the conformational search to torsion space, the energy barriers are made higher and the search space becomes "topologically" more complex as a result. Note that the ECEPP forcefield used by Abagyan has adjusted torsional barrier heights, supposedly to compensate for this. Personally, I think this is comparing apples with oranges until someone can perform an optimization in ALL internal coordinates (including bends, stretches etc. but excluding redundant coordinates) so that the number of degrees of freedom are the same. I suspect, however, that internal coords will win for the reasons stated above. Anybody know of a progam that can do FULL internal coordinate optimization? Richard Gillilan Cornell Theory Center Cartesian <-> internal coordinates: This question has to be answered with is clear "It depends". Usually cartesian coordinates introduces a great deal of undesired couplings. One may get rid of them by choosing the right internal coordinates. My experience is that nothing can beat a well-chosen Z-matrix. Other internal coordinate systems, e.g. Pulays natural internal coordinates compare also very well in the literature. However, the choice of the coordinate system depends -at least in my view- entirely on two things: 1. The nature of the molecule one wishes to optimize. Establishing a Z-matrix for polycyclic systems is a nightmare that nobody really wants to go through. Some people claim that it is impossible to compose a good Z-matrix for such a system. So if the only two options available are cartesians and Z-matrix AND the molecule is unpleasantly complex, cartesians should be preferred. In agreement with this, many papers mention that cartesians are superior to anything else for polycyclic molecules. However, these statements are NOT independent of 2.) 2. The quality of the initial Hessian that is available. Because of the couplings they introduce, cartesians do in general not have the best reputation. However, Baker and Hehre showed that if a good approximation to the Hessian is available, cartesians perform comparably to other sets of internal coordinates. They also stress, that for FLEXIBLE polycyclic systems (whatever that may be) they found the performance of cartesian coordinates to be below internal coordinates. A few of the relevant references are: J.Baker and W.J. Hehre, J.Comp.Chem. 12, 606 (1991) J.Baker, J.Comp.Chem. 14, 1085 (1993) J.Baker and D.Bergeron, J.Comp.Chem. 14, 1339 (1993) P.Pulay and G.Fogarasi, J.Chem.Phys. 96, 2856 (1991) Hope this helps, Folke Folke Noertemann Lehrstuhl f. Theoret. Chemie TU Muenchen noertema@theochem.tu-muenchen.de