From savary@sc2a.unige.ch Fri Oct 14 04:19:50 1994 Received: from UNI2B.UNIGE.CH for savary@sc2a.unige.ch by www.ccl.net (8.6.9/930601.1506) id DAA10326; Fri, 14 Oct 1994 03:54:49 -0400 Received: from PCC2333F (129.194.51.63) by uni2b.unige.ch (PMDF V4.3-8 #2502) id <01HI9EEVTBDS00557H@uni2b.unige.ch>; Fri, 14 Oct 1994 08:54:36 WET-DST Date: Fri, 14 Oct 1994 08:54:35 +0100 From: savary@sc2a.unige.ch (Francois Savary) Subject: NewZMat in Gaussian 92 X-Sender: savary@sc2a.unige.ch To: CHEMISTRY@ccl.net Message-id: <01HI9EEWDERM00557H@uni2b.unige.ch> X-Envelope-to: CHEMISTRY@ccl.net MIME-version: 1.0 X-Mailer: Windows Eudora Version 1.4.3b4 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Dear Netters, I want to make a linear synchronous transit between two minima with different symmetries. So the two Z-matrices I have, are not of the same type, and as I should have both Z-matrices specifying the atoms in the same order, how do I employ the NewZMat utility. Can someone help me and give me an example. Thanks in advance, Francois Savary ---------------------------------------------------------------------------- Francois Savary University of Geneva Department of Physical Chemistry CHIFI Weber 30 quai Ernest-Ansermet CH-1211 Geneva 4 Lab : 112 Phone : +4122 702 65 32 Fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch HTML : http://scsg9.unige.ch/tabmat.html (in french) : http://scsg9.unige.ch/eng/toc.html (in english) ---------------------------------------------------------------------------- From makula@bisance.citi2.fr Fri Oct 14 05:19:51 1994 Received: from FRMOP11.CNUSC.FR for makula@bisance.citi2.fr by www.ccl.net (8.6.9/930601.1506) id EAA10592; Fri, 14 Oct 1994 04:39:57 -0400 Received: from galaad.citi2.fr by FRMOP11.CNUSC.FR (IBM VM SMTP V2R2) with TCP; Fri, 14 Oct 94 09:39:35 EST Received: from bisance.citi2.fr by galaad.citi2.fr; (5.65/1.1.8.2/20Jun94-0455PM) id AA10344; Fri, 14 Oct 1994 09:30:42 +0100 Received: by bisance.citi2.fr (5.0/SMI-SVR4) id AA13114; Fri, 14 Oct 1994 09:39:19 --100 From: makula@bisance.citi2.fr (makula-bisance) Message-Id: <9410140839.AA13114@bisance.citi2.fr> Subject: Chelation To: chemistry@ccl.net Date: Fri, 14 Oct 1994 09:39:18 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Content-Length: 341 Dear netters, I am looking for some information or references on the simulation of chelation of metallic ions by organic molecules, using either MM or QM methods. I will summarize for the net. Thanks, Remi Le Goas CAMD Rhone-Poulenc Agrochimie Lyon - France E-mail : remi.le-goas@rp.fr (please do not use the address in the From: line) From tolja@maya.geo.uu.se Fri Oct 14 07:19:52 1994 Received: from columba.udac.uu.se for tolja@maya.geo.uu.se by www.ccl.net (8.6.9/930601.1506) id GAA11345; Fri, 14 Oct 1994 06:21:34 -0400 Received: from maya.geo.uu.se.geo (maya.Geo.UU.SE) by columba.udac.uu.se with SMTP id AA38404 (5.67b8/IDA-1.4.4 for CHEMISTRY@ccl.net); Fri, 14 Oct 1994 11:21:26 +0100 Received: by maya.geo.uu.se.geo (4.1/SMI-4.1) id AA14150; Fri, 14 Oct 94 11:14:37 +0100 Date: Fri, 14 Oct 94 11:14:37 +0100 From: tolja@maya.geo.uu.se (Anatoli Belonoshko) Message-Id: <9410141014.AA14150@maya.geo.uu.se.geo> To: CHEMISTRY@ccl.net Subject: pointers to nice animations? X-Charset: LATIN1 X-Char-Esc: 29 Dear CCLers, I am preparing kind of intro-lecture for our students and will appreciate if you could provide me with cyberspace coordinates of nice animations, preferably of inorganic type systems, like solids (crystal), melts and /or phase transformations. I was trying to search with archie and veronica but have found surprisingly few. Animations might be in any suitable for PC IBM compatible format (avi, fli, mpg ...) If there are animations with sound it would be even better. Please write directly to me. In case of significant interest I will post the list of available animations to the list. Thank you. Anatoly Belonoshko Uppsala University, Sweden e-mail: tolja@maya.geo.uu.se From waller@thor.herl.epa.gov Fri Oct 14 09:21:13 1994 Received: from thor.herl.epa.gov for waller@thor.herl.epa.gov by www.ccl.net (8.6.9/930601.1506) id IAA12117; Fri, 14 Oct 1994 08:21:54 -0400 Received: by thor.herl.epa.gov (931110.SGI/1.34) id AA14503; Fri, 14 Oct 94 05:32:40 -0400 Date: Fri, 14 Oct 1994 05:32:40 -0400 (EDT) From: "Dr. Chris L. Waller" Subject: PB-PK Summary To: COMP CHEM Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks to all who replied! In short, there are quite a few packages in use. ACSL and SimuSolv which I mentioned in the original posting and... MATLAB with the Simulink Module (contact henk@qsar.ritox.dgk.ruu.nl) Scientist (from ACS software) Stella (from High Performance Systems) and of course, RS/1, SAS, Autoan/Nonlin. I have decided to test Stella. This package apparently runs on PCs and Macs, has a very flexible and intuitive graphical interface, and is relatively inexpensive (a rare commodity these days). I will be willing to share my experiences with all interested parties. CW ******************************************************************** *Chris L. Waller, Ph.D. PHONE 919-541-7976* *Research Chemist FAX 919-541-5394* *waller@thor.herl.epa.gov * *Pharmacokinetics Branch (MD-74) * *ETD/HERL/USEPA * *Research Triangle Park, NC 27711 * * * *Disclaimer: Mention of trade names or products does not constitute* *endorsement by the United States Environmental Protection Agency. * ******************************************************************** From YQIN@aardvark.ucs.uoknor.edu Fri Oct 14 11:20:21 1994 Received: from aardvark.ucs.uoknor.edu for YQIN@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.9/930601.1506) id LAA15845; Fri, 14 Oct 1994 11:03:25 -0400 From: Message-Id: <199410141503.LAA15845@www.ccl.net> Date: Fri, 14 Oct 94 10:04 CDT Subject: 2D graphic software To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear netters: Can anybody tell me where I can get free 2D graphic software like Xvgb or other "easy and friendly" to deal with. Thank you very much for your help. Best ragards yue qin yqin@aardvark.ucs.ouknor.edu From ashy@rose.chem.wesleyan.edu Fri Oct 14 15:20:18 1994 Received: from rose.chem.wesleyan.edu for ashy@rose.chem.wesleyan.edu by www.ccl.net (8.6.9/930601.1506) id PAA21605; Fri, 14 Oct 1994 15:13:57 -0400 Received: by rose.chem.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA12963; Fri, 14 Oct 1994 15:06:24 -0400 Date: Fri, 14 Oct 1994 15:06:24 -0400 Message-Id: <9410141906.AA12963@rose.chem.wesleyan.edu> From: Ashwin Dinakar To: szeinfel@snfma1.if.usp.br Cc: cletner@remcure.bmb.wright.edu, CHEMISTRY@ccl.net In-Reply-To: (message from Rafael Iosef Najmanovich Szeinfeld {S on Thu, 13 Oct 1994 09:25:08 -0300 (EST)) Subject: Re: CCL:Quantum text Apart from the other books that have been recommended for quantum mechanics I find the Feynman Lectures on Physics-Vol. III a very good book for refreshing on the fundamentals. Ashwin Dinakar, Wesleyan University. From haney@netcom.com Fri Oct 14 18:20:00 1994 Received: from netcom6.netcom.com for haney@netcom.com by www.ccl.net (8.6.9/930601.1506) id SAA24559; Fri, 14 Oct 1994 18:07:21 -0400 Received: by netcom6.netcom.com (8.6.9/Netcom) id PAA18950; Fri, 14 Oct 1994 15:05:08 -0700 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199410142205.PAA18950@netcom6.netcom.com> Subject: Help on SHAKE constraints To: CHEMISTRY@ccl.net, amber@cgl.ucsf.edu, charmm-bbs@emperor.harvard.edu Date: Fri, 14 Oct 1994 15:05:07 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 725 Molecular Dynamics Experts: I wish to ask about the use of constraints like SHAKE in molecular dynamics. What are the reasons that one would use SHAKE? What are the deficiencies of SHAKE? When SHAKE (or the like) is used and you experience problems: 1)What are the symptoms of "failure"?, 2)Under what conditions does this failure occure? and 3)What is the workaround for this failure? -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** From CHEM86@Jetson.UH.EDU Fri Oct 14 21:20:02 1994 Received: from Elroy.UH.EDU for CHEM86@Jetson.UH.EDU by www.ccl.net (8.6.9/930601.1506) id UAA25321; Fri, 14 Oct 1994 20:21:07 -0400 From: Received: from Jetson.UH.EDU by Jetson.UH.EDU (PMDF V4.3-10 #5185) id <01HIA09Z6ZJK91VT89@Jetson.UH.EDU>; Fri, 14 Oct 1994 19:20:59 -0500 (CDT) Date: Fri, 14 Oct 1994 19:20:59 -0500 (CDT) Subject: Pointers in FORTRAN under IRIX - problem solved ! To: chemistry@ccl.net Message-id: <01HIA09Z824I91VT89@Jetson.UH.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT CCL'ers, Many thanks to all who replied to my posting. Your answers helped me a lot to to detach my attention from the allocated memory SIZE problems, and find the real bug I created. Looks like posting to CCL is the best method of debugging ;-) The bug was too early freeing of the allocated memory in one of my procedures. The data in allocated memory still remained perfectly intact, but Unix thought this part of memory is free and the program was killed as soon as ANY statement using malloc call was executed (apparently disk I/O statements belong to this class). I have posted both detailed problem description and its solution to comp.sys.sgi.bugs newsgroup. After removal of one fatal instruction the code runs perfectly and the reward is ~30-fold increase in speed in the case of large inputs. The final conclusion is that Fortran can succesfully use dynamic memory allocation on its own (but it may not be available on all platforms). Thanks again, especially to Peter Shenkin, whose suggestions were very close to the real problem --- Robert Fraczkiewicz Department of Chemistry University of Houston chem86@jetson.uh.edu From raman@bioc01.uthscsa.edu Fri Oct 14 23:20:03 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.9/930601.1506) id WAA27172; Fri, 14 Oct 1994 22:23:08 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Fri, 14 Oct 1994 21:25:35 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA08711; Fri, 14 Oct 94 21:23:19 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9410150223.AA08711@bioc01.uthscsa.edu> Subject: Re: CCL:MAC <-> DOS for MS WORD files To: cgbzd@alinga.newcastle.edu.au (DLUGOGORSKI B Z) Date: Fri, 14 Oct 1994 21:23:18 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <199410030626.QAA07903@alinga.newcastle.edu.au> from "DLUGOGORSKI B Z" at Oct 3, 94 04:26:38 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1313 Bogdan: > Would anyone on the net know how to read MAC files on > a DOS/MSWindows PC? The files were created on a MAC computer > using MS WORD 5.x. Any pointers to commercial/public > domain software will be greatly appreciated. Many thanks. You have two options: (1) Use a hardware/software data conversion setup like DYNAPRO OR (2) Find a QUADRA 610 or an equivalent (I think even a CI would work). This machine can write and read from a PC disk. Once you have it on the PC readable disk, then it is easy to read it from Microsoft WORD for Windows (v 6 or later). Hope this helps Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************