From chemistry-request@server.ccl.net Tue Sep 28 17:21:43 1999 Received: from ursa.calvin.edu (ursa.calvin.edu [153.106.4.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA06216 for ; Tue, 28 Sep 1999 17:21:43 -0400 Received: from GWISE (gwise.calvin.edu [153.106.4.30]) by ursa.calvin.edu (8.8.7/8.8.7) with SMTP id RAA02369 for ; Tue, 28 Sep 1999 17:15:17 -0400 (EDT) Received: from Calvin-Message_Server by GWISE with Novell_GroupWise; Tue, 28 Sep 1999 17:15:18 -0400 Message-Id: X-Mailer: Novell GroupWise 5.5.2 Date: Tue, 28 Sep 1999 17:15:11 -0400 From: "Roger DeKock" To: Subject: Call for Papers - Dynamic Systems in Thermo and Kinetics Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id RAA06217 Call for Papers Please note that the deadline is October 15, 1999 and that submission of abstracts is electronic. COMPUTER MODELING OF DYNAMIC SYSTEMS IN THERMODYNAMICS AND KINETICS To be held at the 219th National American Chemical Society Meeting in San Francisco California, March 26-30, 2000 Sponsored by the Division of Chemical Educatioin (CHED) Abstracts are solicited on new ways of teaching chemical thermodynamics and/or chemical kinetics by means of computer software. We particularly want to emphasize software that provides a visual interface to help the student grasp abstract concepts. An example is Stella®. Users of specialized software for chemistry, such as EQS4WIN® or Chemical Kinetics Simulator® are also encouraged to contribute to this symposium. Other software could include making use of computer algebra systems such as Mathcad®, Mathematica®, or Maple®. Emphasis will be on exercises that students can do, rather than simply on tools that can be used in the classroom. The level of material can range from first year to fourth year. If you have been developing some material that you feel would interest the wider education community, please consider submitting an abstract. Please use the On-line Abstract System (OASys) to submit your abstracts. At http://acs.confex.com/acs/219nm/ched/papers/index.cgi , select the symposium with the above title. The deadline for submitting abstracts is October 15, 1999. Other web sites that you may find useful are: http://www.acs.org http://acs.confex.com/oasys.htm Although use of the OASys is strongly encouraged for your abstract submission, should you have difficulties with the OASys, feel free to E-mail me an electronic copy of your abstract by filling out the word template that a be downloaded at http://www.acs.org/meetings/abstract/absdown.html Computer Modeling of Dynamic Systems in Thermodynamics and Kinetics. Roger L. DeKock: Department of Chemistry and Biochemistry, Calvin College 3201 Burton St. S.E., Grand Rapids, MI 49546-4388, USA (616)957-6344, Fax (616) 957-6501, email: dekock@calvin.edu. From chemistry-request@server.ccl.net Wed Sep 29 04:56:13 1999 Received: from fecit-gate.fecit.co.uk (fecit-gate.fecit.co.uk [194.203.42.250]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA09854 for ; Wed, 29 Sep 1999 04:56:13 -0400 Received: by fecit-gate.fecit.co.uk; id JAA10349; Wed, 29 Sep 1999 09:51:50 +0100 Received: from unknown(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V5.0) id xma010347; Wed, 29 Sep 99 09:51:14 +0100 Received: from fecit.co.uk (NT2.fecit.co.uk [192.168.101.107]) by suisei.fecit.co.uk (8.6.9/8.6.9) with ESMTP id JAA05527 for ; Wed, 29 Sep 1999 09:54:08 +0100 Message-ID: <37F1D1F3.1CD1E957@fecit.co.uk> Date: Wed, 29 Sep 1999 09:46:43 +0100 From: Herbert Fruchtl Organization: Fujitsu European Centre for Information Technology X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: Re: CCL:Linux distributions and FORTRAN (g77) References: <19990927133440.2952.qmail@nwcst314.netaddress.usa.net> <99092811365803.26649@bacchus.pc1.uni-duesseldorf.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jochen wrote: > > > >that (1) use f2c instead (2) manually change all single precision > >variables to double that is laborious or (3) obtain free full > > sed s/real/real*8/ It ain't that easy. Most compilers don't allow a 'real*8 function', and you may hit the 72-column limit. Nevertheless, there are (free) tools available. I'd start searching at the Fortran Market: http://www.uni-comp.com/fortran/ Regards, Herbert From chemistry-request@server.ccl.net Wed Sep 29 08:32:12 1999 Received: from mail.ceniai.inf.cu (ceniai.net.cu [169.158.128.142]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA11713 for ; Wed, 29 Sep 1999 08:31:59 -0400 Received: from int.ceniai.inf.cu (ceniai.inf.cu [169.158.128.138]) by mail.ceniai.inf.cu (8.9.3/8.9.3) with ESMTP id IAA04824 for ; Wed, 29 Sep 1999 08:21:43 GMT Received: (from uucp@localhost) by int.ceniai.inf.cu (8.9.3/8.9.3) with UUCP id IAA06957 for chemistry@ccl.net; Wed, 29 Sep 1999 08:24:54 -0400 (CDT) Received: from ceinpet.inf.cu ([192.168.1.188]) by hermes.ceinpet.inf.cu (8.8.7/8.8.7) with ESMTP id IAA01218 for ; Wed, 29 Sep 1999 08:10:20 -0400 Sender: rgrau@hermes.ceinpet.inf.cu Message-ID: <37F20109.9883C382@ceinpet.inf.cu> Date: Wed, 29 Sep 1999 08:07:37 -0400 From: Ricardo Grau Crespo Organization: CEINPET X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary: pyridine in zeolites Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, Some days ago I posted this question: >Can anyone point me to references on computational studies of pyridine >difussion or sorption in zeolites, preferably ZSM-5? >Any suggestion would be appreciated. I received two answers: ---------------------------------------------------------------- >I did this simulation. The reference is > K. Teraishi, K. Akanuma, Microporous Materials, 11 (1997) p185. > I hope it helps. > > Yours. > > K. Teraishi; Dr. > Nippon Zeon Co. Ltd. ----------------------------------------------------------------- > "Sorption, sorption kinetics and diffusion of pyridine in zeolites" > Bludau_H, Karge_HG, Niessen_W; > Microporous and Mesoporous Materials, 1998, Vol. 22, pp. 297-308 > > regards > German Sastre Navarro ----------------------------------------------------------------- Thanks a lot, Ricardo. Ricardo Grau Crespo Catalysis Division Center for Petroleum Research Cuba From chemistry-request@server.ccl.net Wed Sep 29 03:52:55 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA09513 for ; Wed, 29 Sep 1999 03:52:37 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id JAA01357; Wed, 29 Sep 1999 09:45:22 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Iraj Daizadeh , CCL Subject: Re: CCL:C to Fortran Date: Wed, 29 Sep 1999 09:35:17 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: In-Reply-To: MIME-Version: 1.0 Message-Id: <99092909452201.01303@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA09514 On Die, 28 Sep 1999 Iraj Daizadeh wrote: Jochen Küpper wrote: >> There is the cfortran package to do that portably. >This process is trivial and is essentially unix platform independent. See >my review in the archives-- or for a most trivial example ... see > >http://www.mcb.harvard.edu/gilbert/daizadeh/multi_prog.html Well, some compilers add a underscore, some don't. GCC actually adds _two_ underscores if the fortran name contains one already. What's about strings ? ... This stuff is nicely handled by cfortran. But basically there is no problem in calling C -> FORTRAN or vice versa. I have done that for several projects. If you use an autoconf/automake organized project to be compiled on any exotical system cfortran gets handy, though. And it takes some thinking from people not that familiar with FORTRAN calling conventions. Since I was asked, cfortran is available at http://www-zeus.desy.de/~burow I am not connected to that project at all, besides using it :-) -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Wed Sep 29 04:11:01 1999 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.222.33]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA09696 for ; Wed, 29 Sep 1999 04:11:00 -0400 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 11166 invoked from network); 29 Sep 1999 08:04:18 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 29 Sep 1999 08:04:18 -0000 Received: (qmail 14737 invoked by uid 10283); 29 Sep 1999 08:04:03 -0000 Message-ID: <19990929080403.14736.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: LINUX: g98 test355.com To: chemistry@ccl.net Date: Wed, 29 Sep 1999 10:04:03 +0200 (MSZ) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I compiled g98 on a Linux86 box and did the test suite. Test Job 355 does not do what it should: in the last (third) MCSCF run, it bombs after the third macro-iteration and then obviously does not converge. I used pgf77 with and without the -Mvect directive (which in my experience is dangerous. I do not use any optimized blas library (using blas.F instead). **** LINUX users with a correct test355.log please drop me a note **** I have tailored a Makefile for g77 compilation, but only run a few tests with it. Perhaps I should recompile everything with g77 and try test355.com again. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 700 6485 Theoretical Chemistry | Fax (University): +49 234 709 4109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Wed Sep 29 04:47:19 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA09826 for ; Wed, 29 Sep 1999 04:46:36 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id KAA01560 for ; Wed, 29 Sep 1999 10:39:50 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Computational Chemistry List Subject: CCL:C++ vs Fortran performance Date: Wed, 29 Sep 1999 10:31:54 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: In-Reply-To: MIME-Version: 1.0 Message-Id: <99092910395006.01303@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id EAA09827 Well, I try to give a very cut-down summary: FORTRAN 77 _compilers_ can be better because F77 optimization is NP while C/C++ optimization is not. (There are also aliasing issues, ... but these are way less important.) C's and esp. C++'s data encapsulation, templates, ... provide better possibilities to use inherent knowledge on the problem by using more problem-specific algorithms (it's easier in C++, but basically could done in FORTAN as well, of course - just not as nice). Most important (from my experience) is to get better localisation/patterns of memory access. (Again this can be done in F77 as well, but is usually very ugly.) So - in principle FORTRAN is faster, but in C++ it is easier to code fast programs (faster than usual FORTRAN code). Do you agree ? -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Wed Sep 29 07:31:09 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA11438 for ; Wed, 29 Sep 1999 07:31:07 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id NAA01890; Wed, 29 Sep 1999 13:23:55 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Herbert Fruchtl , chemistry@server.ccl.net Subject: Re: CCL:Linux distributions and FORTRAN (g77) Date: Wed, 29 Sep 1999 13:14:21 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <19990927133440.2952.qmail@nwcst314.netaddress.usa.net> <99092811365803.26649@bacchus.pc1.uni-duesseldorf.de> <37F1D1F3.1CD1E957@fecit.co.uk> In-Reply-To: <37F1D1F3.1CD1E957@fecit.co.uk> MIME-Version: 1.0 Message-Id: <9909291323550B.01303@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id HAA11439 On Mit, 29 Sep 1999 Herbert Fruchtl wrote: >Jochen wrote: >> >> > >that (1) use f2c instead (2) manually change all single precision >> >variables to double that is laborious or (3) obtain free full >> >> sed s/real/real*8/ > >It ain't that easy. Most compilers don't allow a 'real*8 function', and >you may hit the 72-column limit. Well, I should have made clear my intention. Of course the comment wasn't meant to completly solve the problems you encounter with badly designed code. There are sveraly other issues besides variable declarations that might need changes. I am just fed up with people telling me this or that compiler is bad, while they really mean: "I do have some crappy code and this compiler does not fix it automagically." In the first place people should try to have good code - either by writing good code or by obtaining it from somewhere else. And if there is any standard on floating point numbers at all, you have to take IEEE. (But I would actually not rely on any such standard more than any necessary.) Writing code for longerish scientific calculation without thinking about precision issues isn't really good design-practice, and IIRC only Cray does have this 64 Bit single precision real number thing. If code does rely on 64 bit single precision reals, it is designed to run on a Cray and _not_ meant to run on any other platform. (Or it was probably not designed at all.) So please don't blame it on a compiler! -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Wed Sep 29 07:58:21 1999 Received: from granite.sentex.net (granite.sentex.ca [199.212.134.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA11550 for ; Wed, 29 Sep 1999 07:58:21 -0400 Received: from pppuser.uoguelph.ca (p4.xenon.sentex.ca [205.211.164.20]) by granite.sentex.net (8.8.8/8.6.9) with SMTP id HAA15855 for ; Wed, 29 Sep 1999 07:51:45 -0400 (EDT) Message-Id: <4.1.19990929073718.00ba7230@mail.sentex.net> X-Sender: mathtrek@mail.sentex.net X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Wed, 29 Sep 1999 07:40:05 -0400 To: From: "W. R. Smith" Subject: Re: CCL:Call for Papers - Dynamic Systems in Thermo and Kinetics In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id HAA11551 EQS4WIN, mentioned below, is described at http://www.mathtrek.com And while I think of it, another site that might be of interest as regards chem education is http://www.chemical-stoichiometry.net At 05:15 PM 9/28/99 -0400, Roger DeKock wrote: >Call for Papers > >Please note that the deadline is October 15, 1999 and that submission of >abstracts is electronic. > >COMPUTER MODELING OF DYNAMIC SYSTEMS IN THERMODYNAMICS >AND KINETICS > >To be held at the 219th National American Chemical Society Meeting in San >Francisco California, March 26-30, 2000 > >Sponsored by the Division of Chemical Educatioin (CHED) > >Abstracts are solicited on new ways of teaching chemical thermodynamics >and/or chemical kinetics by means of computer software. We particularly >want to emphasize software that provides a visual interface to help the >student grasp abstract concepts. An example is Stella®. Users of >specialized software for chemistry, such as EQS4WIN® or Chemical Kinetics >Simulator® are also encouraged to contribute to this symposium. Other >software could include making use of computer algebra systems such as >Mathcad®, Mathematica®, or Maple®. Emphasis will be on exercises that >students can do, rather than simply on tools that can be used in the >classroom. The level of material can range from first year to fourth year. > >If you have been developing some material that you feel would interest >the wider education community, please consider submitting an abstract. > >Please use the On-line Abstract System (OASys) to submit >your abstracts. At http://acs.confex.com/acs/219nm/ched/papers/index.cgi , >select the symposium with the above title. The deadline for submitting >abstracts is October 15, 1999. > >Other web sites that you may find useful are: > >http://www.acs.org > >http://acs.confex.com/oasys.htm > > >Although use of the OASys is strongly encouraged for your abstract >submission, should you have difficulties with the OASys, feel free to >E-mail me an electronic copy of your abstract by filling out the word >template that a be downloaded at >http://www.acs.org/meetings/abstract/absdown.html > >Computer Modeling of Dynamic Systems in Thermodynamics and Kinetics. >Roger L. DeKock: Department of Chemistry and Biochemistry, Calvin >College 3201 Burton St. S.E., Grand Rapids, MI 49546-4388, USA >(616)957-6344, Fax (616) 957-6501, email: dekock@calvin.edu. > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > -- W. R. Smith, PhD, P. Eng., Senior Scientist, Mathtrek Systems -- 3-304 Stone Road West, Suite 165, Guelph, Ontario CANADA N1G 4W4 EMail: support@mathtrek.com Tel:519-763-1356,FAX:519-763-4525 --------------------- http://www.mathtrek.com --------------------- -Mathtrek Systems - Home of EQS4WIN Chemical Equilibrium Software - From chemistry-request@server.ccl.net Wed Sep 29 11:31:21 1999 Received: from mallard.duc.auburn.edu (mallard2.duc.auburn.edu [131.204.2.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA12929 for ; Wed, 29 Sep 1999 11:31:21 -0400 Received: from localhost (kwonohy@localhost) by mallard.duc.auburn.edu (8.8.8+Sun/8.7.2) with SMTP id KAA14533 for ; Wed, 29 Sep 1999 10:24:44 -0500 (CDT) X-Authentication-Warning: mallard.duc.auburn.edu: kwonohy owned process doing -bs Date: Wed, 29 Sep 1999 10:24:43 -0500 (CDT) From: Ohyun Kwon X-Sender: kwonohy@mallard2 To: chemistry@ccl.net Subject: For symmetry breaking during SCF cycle Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers; Thank you so much for helpful answers to my inquiry. I summarized all of advices on my problem. I appreciate people who were kind to respond to my question. The question is: I am doing ab initio calculations on C5 symmetry molecule using G98 program. However, I found following message. Standard basis: 6-31+G(d) (6D, 7F) There are 243 symmetry adapted basis functions of A symmetry. Standard basis: 6-31+G(d) (6D, 7F) There are 243 symmetry adapted basis functions of A symmetry. Crude estimate of integral set expansion from redundant integrals=1.000. Integral buffers will be 131072 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned on. 243 basis functions 436 primitive gaussians 43 alpha electrons 43 beta electrons nuclear repulsion energy 685.6977012024 Hartrees. One-electron integrals computed using PRISM. NBasis= 243 RedAO= T NBF= 243 NBsUse= 243 1.00E-04 NBFU= 243 Projected CNDO Guess. Requested convergence on RMS density matrix=1.00E-08 within 64 cycles. Requested convergence on MAX density matrix=1.00E-06. Density matrix breaks symmetry, PCut= 1.00E-07 Density has only Abelian symmetry. Density matrix breaks symmetry, PCut= 1.00E-07 Density has only Abelian symmetry. Density matrix breaks symmetry, PCut= 1.00E-07 Density has only Abelian symmetry. Density matrix breaks symmetry, PCut= 1.00E-07 Density has only Abelian symmetry. Density matrix breaks symmetry, PCut= 1.00E-07 Density has only Abelian symmetry. Could anybody give me some advices on this problem? Ny input sections are; # hf/6-31+g* scf=tight opt=z-matrix freq iop(5/13=1) test And I used cartician coordinate for melecular orientation. Thanks. yours Ohyun Kwon Auburn University Auburn, AL, 36849 ------------------------------------------------------------------------- Answers are as follows; ------------------------------------------------------------------------- Dear Dr. Kwon, There are several possible reasons for the breaking of symmetry. First, in Cartesians, your geometry cannot be strictly symmetric. Second, it is possible that one of your degenerate representations becomes unfully occupied (e.g., only 2 rather than 4 electrons). Some other reasons are also conceivable, though, these two could be the main source of your problem. Try to use z-matrix with a dummy atom at the center of molecule so that all symmetrically equivalent atoms be defined in a symmetrically equivalent way. Next, check your occupation numbers and the distribution of electrons over irreps. Best regards Prof. Alexander Bagatur'yants Photochemistry Center, Russian Academy of Sciences ul. Novatorov 7a, Moscow, 117421 Russia Phone: (007-095)-936-2588 Fax: (007-095)-936-1255 E-mail: sasha@icp.rssi.ru Home page: http://www.icp.rssi.ru/eng/bagat/bagat.htm -------------------------------------------------------------------------- Date: Sun, 26 Sep 1999 11:38:32 +0200 (MSZ) From: Christoph.van.Wuellen@ruhr-uni-bochum.de To: Ohyun Kwon Subject: Re: CCL:density matrix breaks symmetry during SCF calc. As far as I know, Gaussian is not designed to exploit non-abelian symmetry groups. If the problem described leads to an error, just distort the five-ring slightly that it only has C2v symmetry (by 0.001 Angstrom). C.v.W. -------------------------------------------------------------------------- Date: Sun, 26 Sep 1999 10:29:23 -0400 (EDT) From: "Dr. Kai Exner" To: Ohyun Kwon Subject: Re: CCL:density matrix breaks symmetry during SCF calc. Dear Ohyun This problem is frequently encountered if diffuse functions are included in the basis set. Try SCF(IntRep,NoVarAcc,Tight). If this doesn't help, be just patient (obstinate?) and let G98 run a wile longer. The chances are high that the SCF will converge in spite of the problem. Good luck Kai -------------------------------------------------------------------- Dr. Kai Exner | phone: 706 542-7515 Ctr. for Comp. Quantum Chem. | fax: 706 542-7514 University of Georgia | e-mail: exner@ccqc.uga.edu Athens, GA 30602-2525 | http://zopyros.ccqc.uga.edu -------------------------------------------------------------------- -------------------------------------------------------------------------- Date: Mon, 27 Sep 1999 11:11:07 +0200 From: Armando Navarro To: Ohyun Kwon Subject: RE:CCL:density matrix breaks symmetry during SCF calc. [The following text is in the "iso-8859-1" character set] [Your display is set for the "US-ASCII" character set] [Some characters may be displayed incorrectly] Hi: You can have two problems, First, you can have a first-order Jahn-Teller instability so the density matrix cannot have the total symmetry (be sure that you does not have partially occupied degenerate orbitals). If this is the problem try to run with the nosymm keyword in order to allow a nonsymmetric wavefunction. Sometimes the wavefunction can have the full symmetry but during the scf cycles the density matrix breaks symmetry, if you have this problem, try to converge the wavefunction with full symmetry with a small basis set such as sto-3g or 3-21g and then project the wavefunction onto your current basisset with guess=read. Best regards Armando Navarro Departamento de quimica organica. Facultade de quimica Universidade de Santiago de Compostela Spain From jkl@ccl.net Wed Sep 29 10:50:53 1999 -0400 Return-Path: Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA27562 for ; Wed, 29 Sep 1999 10:50:50 -0400 (EDT) Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by mserv.rug.ac.be (8.9.0/8.9.0) with ESMTP id QAA00256 for ; Wed, 29 Sep 1999 16:50:35 +0200 (MET DST) Received: (from patrick@localhost) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) id QAA08810; Wed, 29 Sep 1999 16:55:53 +0200 (DFT) Date: Wed, 29 Sep 1999 16:55:52 +0200 (DFT) From: Patrick Bultinck To: jkl@ccl.net Subject: BSSE and chemical ambiguity (fwd) Message-ID: Dear, I have a problem with the following. Say, a quantum chemist wants to calculate the thermodynamic quantities for the following reaction : A-B -> A + B He needs a couple of energies, but also the vibration frequencies. So he goes off to calculate the hessians of all fragments and the complex. A and B should be in a minimum to calculate Delta H (e.g.). The interaction energy is calculated in CP way. But now... He wants to optimize A and B starting from their geometries as they are present in the complex. Option 1 : He optimizes A with A monomer basis set, and similar for B. As such he obtains 'true minima' for A and B, chemically relevant, but looses BSSE correction in Delta-H on the way. Option 2 : He optimizes A and B both separately, but in the supermolecule basis set. BSSE can be corrected for. BUT... who knows in what way the presence of ghost orbitals acts in the optimization ? And what is Delta-H worth chemically for A and B in a minimum that gives rise to chemical question marks ? It is clear that doing optimizations with the supermolecule set, yields some chemical and mathematical ambiguities (also noted and published by Mayer et al.). The matter is getting worse. Consider A a ligand with 50 minima. We need to get the relaxation of A to the global minimum, since that is most occupied, and considering relaxation to say the 41th minimum (the minimum that might resemble the distorted geometry of A best) bypasses some distorion energy and distorsion delta-H. But how do I get to the global minimum from my distorted A geometry when I use the supermolecule set. I could twist a couple of dihedral maybe, but how to twist the ghost orbitals along ;-) ? Am I too bold at saying that the best option is to go for the biggest basis set you can afford, and try to keep BSSE as small as possible (you might get an idea from the interaction energy BSSE correction) ? I have tested cases in which I used both options for small A and B, and found very little difference. But I would like to know how other people would tackle the problem when A and/or B are big, and exhibit a lot of minima. My opinion is to include BSSE in the calculation of the interaction energy, consider distrotion energies in the monomer basis sets (if necessary no problem to calculate using the global minimum as a reference), and calculate thermodynamic quantities also in monomer sets. I admit that my results will have a certain error flag due to not inclusing BSSE corrections, but I think it is chemically still intuitive and correct, and errors originate from an incomplete basis set. The other option corrects for BSSE but bends away (too much ?) from straight chemical relevance and intuition. After all we do not optimize H2O with sodium orbitals 'somewhere' in the neighbourhood if we want to get good vibrational frequencies for free H2O e.g. I agree that the more complete the set the better, but I think that does not allow the use of imbalanced basis sets. Any ideas, Patrick Bultinck Quantum Chemistry Group University of Ghent Belgium From chemistry-request@server.ccl.net Wed Sep 29 11:06:30 1999 Received: from donkeykong.rs.itd.umich.edu (smtp@donkeykong.rs.itd.umich.edu [141.211.63.19]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA12707 for ; Wed, 29 Sep 1999 11:06:30 -0400 Received: from galaxian.rs.itd.umich.edu (smtp@galaxian.rs.itd.umich.edu [141.211.63.92]) by donkeykong.rs.itd.umich.edu (8.8.8/4.3-mailhub) with ESMTP id KAA24458; Wed, 29 Sep 1999 10:59:47 -0400 (EDT) Received: from localhost (brupalf@localhost) by galaxian.rs.itd.umich.edu (8.8.8/5.1-client) with ESMTP id KAA27979; Wed, 29 Sep 1999 10:59:46 -0400 (EDT) Precedence: first-class Date: Wed, 29 Sep 1999 10:59:46 -0400 (EDT) From: Bruce Allan Palfey X-Sender: brupalf@galaxian.rs.itd.umich.edu To: "W. R. Smith" cc: chemistry@ccl.net Subject: Re: CCL:Call for Papers - Dynamic Systems in Thermo and Kinetics In-Reply-To: <4.1.19990929073718.00ba7230@mail.sentex.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id LAA12708 While we're on the topic... I've collected a list of links to a variety of programs and data that are useful in kinetics/thermodynamics research or teaching that emphasizes doing data analysis or simulation. The list is aimed at what an enzymologist might want, but since that covers a lot of chemistry, there may be wide applicability. Go to: http://www.med.umich.edu/biochem/enzresources/ ciao, Bruce On Wed, 29 Sep 1999, W. R. Smith wrote: > EQS4WIN, mentioned below, is described at > > http://www.mathtrek.com > > And while I think of it, another site that might be of interest as regards > chem education is > > http://www.chemical-stoichiometry.net > > > At 05:15 PM 9/28/99 -0400, Roger DeKock wrote: > >Call for Papers > > > >Please note that the deadline is October 15, 1999 and that submission of > >abstracts is electronic. > > > >COMPUTER MODELING OF DYNAMIC SYSTEMS IN THERMODYNAMICS > >AND KINETICS > > > >To be held at the 219th National American Chemical Society Meeting in San > >Francisco California, March 26-30, 2000 > > > >Sponsored by the Division of Chemical Educatioin (CHED) [---------- long quote from past messages deleted by CCL admin, jkl@ccl.net, [---------- To check conferencee announcements, go to: [---------- http://www.ccl.net/chemistry/announcements/conferences/ From chemistry-request@server.ccl.net Wed Sep 29 10:55:41 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA12637 for ; Wed, 29 Sep 1999 10:55:40 -0400 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA27505 for ; Wed, 29 Sep 1999 10:48:57 -0400 (EDT) Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.8.8/jtpda-5.3) with ESMTP id QAA27679 ; Wed, 29 Sep 1999 16:48:54 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.8.7/8.8.7) id QAA03165; Wed, 29 Sep 1999 16:53:00 +0200 Date: Wed, 29 Sep 1999 16:53:00 +0200 Message-Id: <199909291453.QAA03165@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: hinsen@dirac.cnrs-orleans.fr To: taop@csb0.IPC.PKU.EDU.CN CC: chemistry@www.ccl.net In-reply-to: (message from Tao Peng on Tue, 28 Sep 1999 20:32:21 -0700 (PDT)) Subject: Re: CCL:How to call a C++ program from C? References: > I have a big program which is written in C and Fortran, but mainly in C. > The author compile each module by their own compiler ( cc and f77 on SGI) > and link them by f77. > > Now I have another C++ program (still others) and want incorporate it > into the previous big program. This is difficult, and certainly not possible in a portable way. Mixing C and Fortran is easy, but you should use f77 to link (on some systems this is not strictly necessary; adding the Fortran libraries when linking is sufficient). Mixing C and C++ is also easy, but you must use CC to link. So for mixing C with C++ and Fortran, you'd have to link with both CC and f77. The reason for this problem is that both C++ and Fortran program often need specific initialization code that is added during linking. An added complication with C++ is name mangling (the compiler must create unique names for overloaded functions etc.), but there are ways around that. In summary, what you are trying to do is possible only on a system that allows calling Fortran from C without any special initialization code for Fortran. I don't know whether this is true for SGI systems. -- ------------------------------------------------------------------------------- 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 chemistry-request@server.ccl.net Wed Sep 29 10:43:39 1999 Received: from bobino.sefmedia.com (bobino.sefmedia.com [207.164.6.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA12567 for ; Wed, 29 Sep 1999 10:43:37 -0400 Received: from ppp-5800-01a-3198.mtl.total.net (ppp-5800-01a-3198.mtl.total.net [216.210.30.198]) by bobino.sefmedia.com (NTMail 4.30.0013/NT6102.00.ff403942) with ESMTP id otwcaaaa for ; Wed, 29 Sep 1999 10:36:54 -0400 Reply-To: From: "Bill Hayden" To: Subject: MOE for Academics Date: Wed, 29 Sep 1999 10:31:54 -0400 Message-ID: <000c01bf0a87$60504800$c40101c0@zman> 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 8.5, Build 4.71.2173.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Importance: Normal ******************************** CCG ANNOUNCES SPECIAL PRICING OF THE MOLECULAR OPERATING ENVIROMENT FOR THE ACADEMIC COMMUNITY. Chemical Computing Group Inc. is pleased to make its chemical computing software, MOE - the Molecular Operating Environment, more available to members of the academic community. We will be providing academic researchers MOE's full range of capabilities and functionality, but at a greatly discounted pricing schedule. MOE delivers academic researchers: * A customizable environment allowing for quick prototyping of new ideas and the ability to create your own end applications; * A unique teaching tool that allows your students to "look under the hood" at the underlying algorithms; * Out-of-the-box functionality covering the spectrum of drug research delivering powerful ready-to-use applications in the areas of: HTS, Combichem, protein/homology modeling, modeling & simulations and methods development. * Platform independence: MOE runs native on SGI, Sun, WinNT, Win 95, 98 and DEC Alpha NT Academic researchers are invited to contact: Bill Hayden at 514 393 1055 or email him at hayden@chemcomp.com to find out more about how they can obtain a FREE 30 day evaluation copy of MOE. http://www.chemcomp.com Thanks, Bill William A. Hayden Vice President Chemical Computing Group hayden@chemcomp.com http://www.chemcomp.com 514 393 1055 -phone 514 874 9538 - fax From chemistry-request@server.ccl.net Wed Sep 29 14:18:03 1999 Received: from wirehead.arqule.com (email.arqule.com [207.252.12.140]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA13635 for ; Wed, 29 Sep 1999 14:18:00 -0400 Received: by WIREHEAD with Internet Mail Service (5.5.2650.10) id ; Wed, 29 Sep 1999 14:08:08 -0400 Message-ID: <6B00FB949906D211A88800104B8AE520F41A0E@WIREHEAD> From: "Czerminski, Ryszard" To: "Ccl (E-mail)" , "'gsl-discuss@sourceware.cygnus.com'" , "'matrix-sig@python.org'" Subject: Re: combinations (summary) Date: Wed, 29 Sep 1999 14:08:07 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.10) Content-Type: multipart/mixed; boundary="----_=_NextPart_000_01BF0AA5.94F84666" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_000_01BF0AA5.94F84666 Content-Type: text/plain; charset="iso-8859-1" I would like to express my appreciation to the people who took time to help me with combinations problem: Tim Peters - for Python code which does EXACTLY what I wanted, for advise and for pointers to GNU's GMP package Mirek Gorski - for pointer to GNU's GMP package http://www.math.iastate.edu/cbergman/crypto/gmp/gmp_toc.html Pat Walters - for C++ class for generating combinations Emili Besalu - for pointer to his web page dealing with similar problems http://iqc.udg.es/~emili/emili_nc.htm Thank you all very much! -- Ryszard ORIGINAL QUESTION: I am looking for a function which could compute combinations given lexicographical index e.g. C(1;3,2) -> 1,2 C(2;3,2) -> 1,3 C(3;3,2) -> 2,3 I have found function which does this ( http://math.nist.gov/GAMS.html ) but it is limited to small numbers since it is using regular 4 bytes representation for integers and therefore index range is severly limited ( < 2^32 ). Any pointers to the software which does this for integers of arbitrary length would be very much appreciated. Ryszard Czerminski phone: (781)395-1269 x 479 ArQule, Inc. e-mail: ryszard@arqule.com 200 Boston Avenue http://www.arqule.com Medford, MA 02155 P.S. >from Tim Peters: > I am looking for a function which could compute > combinations given lexicographical index e.g. > > C(1;3,2) -> 1,2 > C(2;3,2) -> 1,3 > C(3;3,2) -> 2,3 > > I have found function which does this > ( http://math.nist.gov/GAMS.html ) but it is limited > to small numbers since it is using regular 4 bytes > representation for integers and therefore index > range is severly limited ( < 2^32 ). As is often the case, relaxing such limits creates other problems; in this case, the Fortran TOMS 515 algorithm recomputes the number of combinations >from scratch each time thru the inner loop, which is very expensive if choosing many elements from a very large set. > Any pointers to the software which does this for > integers of arbitrary length would be very much > appreciated. One is attached. Note that since this is Python instead of Fortran, everything is 0-based. That is, when asking for the i'th combination of m things taken n at a time, i ranges from 0 up to but not including C(m, n), and the "canonical set" is taken to be range(m). The inner loop avoids the problem above, so this is reasonably fast even for multi-hundred digit indices. more-combinations-than-a-reasonable-person-could-want-ly y'rs - tim def _chop(n): """n -> int if it fits, else long.""" try: return int(n) except OverflowError: return n def comb(m, n): """m, n -> number of combinations of m items, n at a time. m >= n >= 0 required. """ if not m >= n >= 0: raise ValueError("m >= n >= 0 required: " + `m, n`) if n > (m >> 1): n = m-n if n == 0: return 1 result = long(m) i = 2 m, n = m-1, n-1 while n: # assert (result * m) % i == 0 result = result * m / i i = i+1 n = n-1 m = m-1 return _chop(result) def combatindex(m, n, i): """m, n, i -> i'th combination of m items taken n at a time. m >= n >= 1 and 0 <= i < comb(m, n) required. Return the i'th combination in lexicographic order, as a list of n elements taken from range(m). The index (i) is 0-based. Example: >>> for i in range(6): ... print combatindex(4, 2, i) [0, 1] [0, 2] [0, 3] [1, 2] [1, 3] [2, 3] """ if not m >= n >= 1: raise ValueError("m >= n >= 1 required: " + `m, n`) c = long(comb(m, n)) if not 0 <= i < c: raise ValueError("0 <= i < comb(m,n) required: " + `i, c`) result = [] # have c == comb(m, n), want comb(m-1,n-1) c = c * n / m # invariant: c == comb(m-1, n-1) for element in xrange(m): if i < c: # take this element, and n-1 from the remaining result.append(element) n = n-1 if n == 0: break # have c == comb(m-1,n), want comb(m-2,n-1) c = c * n / (m-1) else: # skip this element, and take all from the remaining i = i-c # have c == comb(m-1,n-1), want comb(m-2,n-1) c = c * (m-n) / (m-1) m = m-1 assert i == 0 return result def _test(): failures = 0 m, n = 10, 6 c = comb(m, n) last = [0] * n for i in xrange(c): this = combatindex(m, n, i) if len(this) != n: print "*** length error:", m, n, i, this failures = failures + 1 if not last < this: print "*** lexicographic error:", m, n, i, last, this failures = failures + 1 last = this if this != range(m-n, m): print "*** last value wrong:", m, n, c-1, this failures = failures + 1 # c has more than 1400 digits in the next case -- may take a # few seconds m, n = 5000, 2000 c = comb(m, n) this = combatindex(m, n, 0) if this != range(n): print "*** first value wrong:", m, n, 0, this failures = failures + 1 this = combatindex(m, n, c-1) if this != range(m-n, m): print "*** last value wrong:", m, n, c-1, this failures = failures + 1 if failures: print "*********** TEST FAILED *************" if __name__ == "__main__": _test() ========================================================= >from Pat Walters: ------_=_NextPart_000_01BF0AA5.94F84666 Content-Type: application/octet-stream; name="combo.cpp" Content-Disposition: attachment; filename="combo.cpp" #include #include #include #include using namespace std; #include "combo.h" // Combination generator class // Takes a vector of integers as input and generates // all combinations /* int main(int argc, char *argv[]) { vector b(3); b[0] = 2; b[1] = 3; b[2] = 2; combo c(b); while (!c.done()) { print_v(c.get_current()); c.next(); } return(0); } Produces 0 0 0 0 0 1 0 1 0 0 1 1 0 2 0 0 2 1 1 0 0 1 0 1 1 1 0 1 1 1 1 2 0 1 2 1 */ // support function to print a vector void print_v(const vector &v) { for (int i = 0; i < v.size(); i++) printf("%4d ",v[i]); printf("\n"); fflush(stdout); } // constructor - takes a vector of ints // each int represents the maximum number of possibilities for // that position. combo::combo(const vector &x) { enough = false; high.resize(x.size()); curr.resize(x.size()); fill (curr.begin(),curr.end(),0); for ( int i = 0; i < x.size(); i++) high[i] = x[i] - 1; len = high.size(); limit = len-1; } // debuging function to show a combination void combo::show() { for (int i = 0; i < curr.size(); i++) printf("%4d ",curr[i]); printf("\n"); fflush(stdout); } // generate the next combination void combo::next() { bool raised; if (curr[limit] high; bool enough; int len; int limit; vector curr; public : combo(const vector &high); void next(); vector &get_current() {return(curr);}; bool done() {return(enough);} void show(); }; void print_v(const vector &v); ------_=_NextPart_000_01BF0AA5.94F84666-- From chemistry-request@server.ccl.net Wed Sep 29 17:26:17 1999 Received: from ozone.umsl.edu (ozone.umsl.edu [134.124.105.185]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA15160 for ; Wed, 29 Sep 1999 17:26:17 -0400 Received: from ozone.umsl.edu (indy1.umsl.edu [134.124.105.162]) by ozone.umsl.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id VAA11115 for ; Mon, 28 Jun 1999 21:10:31 -0700 Sender: anil@ozone.umsl.edu Message-ID: <37F29EA6.6B29A9D0@ozone.umsl.edu> Date: Wed, 29 Sep 1999 16:20:07 -0700 From: "Anil C. Nair" Organization: University of Missouri-St. Louis X-Mailer: Mozilla 4.07 [en] (X11; U; IRIX 6.2 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: peptide conformational search Content-Type: text/plain; charset=x-UNICODE-2-0-UTF-7 Content-Transfer-Encoding: 7bit Dear All, Few days ago I have asked a question regarding the conformer search of small peptides. I have received only one reply. It was from Peter Shenkin (Schrodinger Inc.) regarding the use of Macromodel. I found it very helpful. Thank you very much. I would also like to hear from experts on other Softwares (InsightII, Cerius2, Spartan etc.) for conformational search on poly-peptides. Thank you. Anil I am copying below my original question and the replys from Peter Shenkin. My Question: ---------- Dear all, I have a set 10-15 peptide molecules (with +AH4-10 aminoacid residues). I would like to generate all possible low energy conformations. I shall appreciate your suggestion regarding the best suitable software (insightII, sybyl, cerius2, spartan etc.) to do this. Also what is the best option to do the conformational search? Is it important to include solvents? Any suggestion/help in this respect will be highly appreciated. Thank you. Anil ________________ Peter Shenkin's Relpy: ----------------- Peter Shenkin wrote: > Hi, > > Our MacroModel software has numerous options for conformational > search and supports a variety of forcefields. Best algorithm > for genreal purposes we now believe to be a mixture of LMCS > (low-mode conformational search) and MCMM (which uses random > torsional moves). > > Hope this helps, > -P. > > > ** Whether the playing field is level depends on the coordinate system. *** > ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* > *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** Also another detailed reply from Peter Shenkin: Peter Shenkin wrote: Hi, Go to ENRGY in the GUI. Select a forcefield (I recommend AMBER94 if it's just a peptide, or MMFF if it's modified or if you expect to study other kinds of molecules as part of the same study). And a minimizer (try either PRCG or TNCG). Go to CSRCH. Request an MCarlo search, automatic setup. You might like to then selects "LowMode". This uses a mixture of torsional degrees of freedom and the new low-mode search method -- we have found the combination very efficacious. Go back to MINIM mode of ENERGY. Select "Start". This will typically run 1000 steps of search -- not nearly enough. You'll typically have a good sense you're done when all low-lying conformations are multiply populated. You can start up new searches >from the shell, using the output of old searches. (Ie, take the .out file from your first search and use it as the .dat file for your new search.) This will accumulate statistics. For all runs past the first one, you'll probably want to start the back end (BatchMin) from the shell. This is covered in the first few chapters of the BatchMin Reference Manual. You'll also find that looking up the commands the GUI generated in the Manual will give you hints for how to change them; for example, how to increase the max. number of steps a mininmization is allowed to take, or the number of steps in a search. This should be enough to get you started. -P. -- ** Whether the playing field is level depends on the coordinate system. *** ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** -- -------------------------------------------------------------- Anil C. Nair | Computational Chemistry Group | Phone :(314)-516-6882 Department of Chemistry | University of Missouri-St. Louis | Fax :(314)-516-5342 8001 Natural Bridge Rd. | St. Louis, MO 63121-4499, USA. | e-mail :anil@ozone.umsl.edu -------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Sep 29 19:30:25 1999 Received: from si.fi.ameslab.gov (si.fi.ameslab.gov [147.155.20.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA16011 for ; Wed, 29 Sep 1999 19:30:25 -0400 Received: (from pradipta@localhost) by si.fi.ameslab.gov (AIX4.2/UCB 8.7/8.7) id SAA24836 for chemistry@ccl.net; Wed, 29 Sep 1999 18:27:07 -0500 (CDT) From: Pradipta Bandyopadhyay Message-Id: <199909292327.SAA24836@si.fi.ameslab.gov> Subject: solvation energy of Glycine! To: chemistry@ccl.net (CCL) Date: Wed, 29 Sep 1999 18:27:06 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Hi everyone, I am interested in the solvation energy of Glycine. Though there are many works on this I am confused by the different results obtained by different solvation models. So, can anyone tell me what is the best estimate of solvation energy of Glycine computationaly? Also, where can I find the best solvation energy of glycine experimentally? I found the simple SCRF ( only dipole term) is absolutely wrong- is it correct or I am making some mistakes? I will summarize. Thanks. Pradipta -- ***************************************** * Dr. Pradipta Bandyopadhyay * * AMES LAB * * Department of Chemistry * * Iowa State Unievrsity * * Ames, IA 50011 * * USA * * e-mail: pradipta@si.fi.ameslab.gov * * Phone : 515-294-4604 (Lab) * * : 515-232-8067 (Residence) * * Fax : 515-294-0105 * * URL: http://www.msg.ameslab.gov/ * * Group/pradipta/index.html * ***************************************** ------------------------------------------------------------------------------ ...FOR AFTERWARDS A MAN FINDS PLEASURE IN HIS PAINS, WHEN HE HAS SUFFERED LONG AND WANDERED FAR. -- HOMER ------------------------------------------------------------------------------ From chemistry-request@server.ccl.net Wed Sep 29 23:23:35 1999 Received: from cyber.iitkgp.ernet.in ([203.197.98.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA16783 for ; Wed, 29 Sep 1999 23:23:27 -0400 From: rajarshi@cts.iitkgp.ernet.in Received: from iitkgp by cyber.iitkgp.ernet.in (5.65v3.2/1.1.10.5/17Aug99-0147PM) id AA28604; Thu, 30 Sep 1999 08:47:56 +0500 Received: from cts.iitkgp.ernet.in by iitkgp.ernet.in (SMI-8.6/SMI-SVR4) id IAA23662; Thu, 30 Sep 1999 08:44:14 +0530 Received: from localhost (rajarshi@localhost) by cts.iitkgp.ernet.in (8.8.7/8.8.7) with SMTP id IAA00534; Thu, 30 Sep 1999 08:48:48 +0530 Date: Thu, 30 Sep 1999 08:48:48 +0530 (IST) To: Jochen Cc: Computational Chemistry List Subject: Re: CCL:C++ vs Fortran performance In-Reply-To: <99092910395006.01303@bacchus.pc1.uni-duesseldorf.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, could you explain a litle (or refer me to doc's that would) about f77 optimizing NP and C++ not. TIA Rajarshi Guha