From oesterei@hrz.ba-freiberg.de Mon Apr 25 04:31:23 1994 Received: from orion.hrz.ba-freiberg.de for oesterei@hrz.ba-freiberg.de by www.ccl.net (8.6.4/930601.1506) id EAA10745; Mon, 25 Apr 1994 04:23:49 -0400 Message-Id: <199404250823.EAA10745@www.ccl.net> Received: by orion.hrz.ba-freiberg.de (16.6/15.6) id AA02642; Mon, 25 Apr 94 10:20:50 +0200 From: Ralf Oestereich Subject: Ethylen calculation with GAMESS To: CHEMISTRY@ccl.net Date: Mon, 25 Apr 94 10:20:49 MESZ Mailer: Elm [revision: 66.25] Concerning GAMESS (US-Version 92)... We have the following problem (and dont laugh! :-) ): We want to minimize energy of the ethylen molecule to get firm with the programm, so we must create a z-Matrix, but ... We are not able to create a z-Matrix for Ethylen! What GAMESS do is, that it creates the z z-axis in the C-H bond, if we have the following $DATA Group: $DATA X C 1 rCX H 2 rCH aXCH rCX=0.67 rCH=1.06 aXCH=120 $END It wont even work without the Dummy! If you have any idea, please mail us! at: oesterei@orion.hrz.ba-freiberg.de From batra@urz.unibas.ch Mon Apr 25 04:45:20 1994 Received: from chx400.switch.ch for batra@urz.unibas.ch by www.ccl.net (8.6.4/930601.1506) id EAA10766; Mon, 25 Apr 1994 04:27:07 -0400 X400-Received: by mta chx400.switch.ch in /PRMD=switch/ADMD=arcom/C=CH/; Relayed; Mon, 25 Apr 1994 10:26:31 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Mon, 25 Apr 1994 11:26:03 +0200 Date: Mon, 25 Apr 1994 11:26:03 +0200 X400-Originator: batra@urz.unibas.ch X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=SWITCH/ADMD=ARCOM/C=CH/;940425102603] X400-Content-Type: P2-1984 (2) Content-Identifier: 95 Conversion: Prohibited Alternate-Recipient: Allowed From: Rohit Batra Message-ID: <95*/S=batra/OU=urz/O=unibas/PRMD=SWITCH/ADMD=ARCOM/C=CH/@MHS> To: CHEMISTRY Subject: Summary: PARALLEL abinitio Dear Netters, A couple of days ago I sent the following message to the list: > Dear Netters, > > Does anyone know about ab initio packages which can optimize open shell > species (UHF-, UMP2-Wavefunctions) **PARALLEL** on distributed memory > machines? > Should there be any responses please reply to me personally I will > summarize and send the summary to the list. > > Thanks a lot, > > Rohit Batra I would like to thank all the netters who replied so promptly and helpfully. Below is a summary of their responses. =============================================================================== Gernot Katzer writes: GAMESS does this for RHF, ROHF, UHF and GVB wave functions. Energy (conventional or direct) and Gradient parallelize very well (Speedup of more than 3.5 with 4 Processors is possible), analytic hessians, however, are problematic, because of high disk demand and unparallelized CP-HF. MC-SCF wave functions can run parallel only in parts. Hope that helps. If you want to have more information, contact me. Gernot Katzer =============================================================================== Tom writes: Hi, Parallel-GAMESS will do the UHF optimization in parallel on a bunch of different parallel platforms. To date, we have run it on an IBM SP1, KSR-1, CM-5, Paragon, iPSC/860, and the Iowa State folks have run it across heterogeneous Ethernetworks of UNIX workstations. I believe there exists a version for the nCUBE. The above refers t the US version of GAMESS. I also believe there is good parallel capability in the UK version, although I have not used it. Tom =============================================================================== Craig Wilson writes: I think that Gaussian 92 is available as a parallel processing package. It will certainly do UHF and UMP2 anyway. Contact Gaussian Inc. 4415 Fifth Avenue, Pittsburgh, PA. 15213 U.S.A for more details. I don't know about specific e-mail addresses, but root@gaussian.com would get through, I guess. Craig Wilson =============================================================================== Swamy Kandadai writes: Rohit: Dr. Michel Dupuis's code HONDO is parallelized for distributed computing environment. Please contact him for a copy of HONDO running in parallel on IBM's Risc sytem 6000. Thanks Swamy =============================================================================== Theresa writes: GAMESS (the US version) is currently parallelized for UHF (and several other) wavefunctions. The UMP2 is not yet parallelized (although the RMP2 is). GAMESS also does not yet have the capability to do any MP2 optimizations except in a very crude manner. The code is free but you do need to sign a "release" form stating that you will not distribute the code. To get a copy, send an e-mail to Mike Schmidt at mike@si.fi.ameslab.gov. If you need any other information, please feel free to contact me. Theresa Windus Department of Chemistry e-mail: windus@chem.nwu.edu Northwestern University Evanston, IL 60208 USA From vkitzing@sunny.mpimf-Heidelberg.mpg.de Mon Apr 25 07:31:21 1994 Received: from foxy.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-Heidelberg.mpg.de by www.ccl.net (8.6.4/930601.1506) id HAA11811; Mon, 25 Apr 1994 07:13:28 -0400 Received: from sunny.mpimf-heidelberg.mpg.de by foxy.mpimf-heidelberg.mpg.de (5.65+/1.34) id AA02821; Mon, 25 Apr 94 13:12:29 +0200 Received: from [192.109.43.34] (mac10) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA22991; Mon, 25 Apr 94 13:08:26 +0200 Date: Mon, 25 Apr 94 13:08:26 +0200 Message-Id: <9404251108.AA22991@sunny.mpimf-Heidelberg.mpg.de> To: "Srinivasan S. Iyengar" From: vkitzing@sunny.mpimf-Heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:helix dipole Cc: CHEMISTRY@ccl.net (Computational Chemistry List) >In his mail Rafael Najmanovich says : >> >> For each pair of opposite charges in the helix you have a dipole >> momentum vector that points from the positive to the negative charge so I >> suppose the total dipole momenta vector of that helix will be the >> vectorial sum of all these vectors. How to calculate it in practice (that >> is, if there are approximation methods or computer algorhitms) I don't know. >> > > I beg to differ. I would rather - > (a) Find the center of mass of all the positive charges. > (b) Find the center of mass of all the negative charges. > (c) Find the dipole moment between these two points. As long as the helix is electrically neutral both results should agree! ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizische Forschung Jahnstr. 29, D69120 Heidelberg, FRG Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat) FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de From h.rzepa@ic.ac.uk Mon Apr 25 07:42:33 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id GAA11721; Mon, 25 Apr 1994 06:40:08 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <21088-0@punch.ic.ac.uk>; Mon, 25 Apr 1994 11:39:04 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA26260; Mon, 25 Apr 94 11:39:34 +0100 Message-Id: <9404251039.AA26260@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 25 Apr 1994 11:39:23 +0100 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Global talks, presentations and posters forum How many times have you gone to a conference with parallel sessions, and wanted to be in two places at once? Or missed a speaker for one reason or another? If your presentation can be mounted on a WWW server, why not offer the URL of the talk to a global talks page, and then we can all share the talk! I have started up a home page for this; http://www.ch.ic.ac.uk/talks/ This will introduce the concept, and show three entries already added. Registration for the page is via a FORMS entry. Just put entries in all the fields and you will be added automatically to the list. You will need a WWW browser which supports forms (Currently e.g. NCSA Mosaic for X-Windows, V2.4, or WinMosaic 2.0a4. A Mac version is expected soon). Please note the following provisos; 1) Entries are not currently tested. Hence make sure you do not mistype them. 2) To remove an entry, you will have to e-mail me. If I (or others) find that a particular URL does not respond after a suitable period, I reserve the right to remove it. 3) I reserve the right to remove "inappropriate" entries. We are expecting scientifically sound talks which have been/will be presented in public to an audience at a specified location and date. I am prepared to consider conference posters, but only if the organisers have given you permission. 4) Currently there is no attempt to sub divide by subject. If this concept is successful, we may wish to consider doing this. We may also add a separate "poster" category. 5) Readers should be aware that no "peer review" mechanism is currently applied to these talks (other than the fact that they have been or will be presented in public),. There is no "time-stamping" mechanism. It is expected that the authors will in fact edit the talks, correct errors etc if they wish to ensure they do not date. I am happy to consider other aspects of this forum that I might not have thought about, and any other general, legal or ethical issues that might arise! If you do mail me, please put GLOBAL TALKS in the subject field so that I can filter these messages out. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.02, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From Patrick.Bultinck@rug.ac.be Mon Apr 25 08:31:23 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id IAA15074; Mon, 25 Apr 1994 08:28:32 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA26649 (5.67b/IDA-1.5 for ); Mon, 25 Apr 1994 14:28:02 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA20125; Mon, 25 Apr 94 14:25:12 +0200 Date: Mon, 25 Apr 1994 14:25:12 +0200 (MET DST) From: Patrick Bultinck Subject: Atom-Atom partitioning of El. Energy To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 3387 Hello world, To my knowledge there is no option for GAMESS (US) to do atom-atom partitionings of the electronic energy. By this partitioning I mean that the total electronic energy, as can be obtained using the classic (i.e. well known) RHF formula, is split up into different atom-atoms terms (i.e. atom1-atom1, atom1-atom2, and atom2-atom2 for a binuclear molecule.) Because I thought it might be interesting for me to have a look at these terms, I headed off to find out if I could not write a small program to do this, or to change the FORTRAN code of gamess (US) as to fit my needs. However, I am not an experienced programmer in FORTRAN (yet). So I ran into trouble (I have studied the first part of my first book on FORTRAN for the first time), so it is not easy for me change the GAMESS code. Here is what I did... I have always been programmig in Basic, or Pascal or C(++), or some even more exotic languages, so as we have a RS6000 workstation I started writing a C program. I have changed the NPRINT=3 option in the GAMESS code and the rungms executable, so that files are saved with the density, fock and hcore matrices. These files are read in by the program and changed as to yield some temporary files that may be used in calculations. So when I now make a calculation I specify NPRINT=3 and get the normal output file plus a $JOB.at file in which I find the atom-atom parts. Everything is written in a very simple C program, because I needed the results asap, so I did not care for any mumbo-jumbo optimising, or elegance (except for the elegance of using indents and such). All this stuff has been done on the 1991 version of GAMESS (they wouldn't let me change the new one.) My question is now : does anybody have an example of a calculation (with at least 10 **ten** basisfunctions) so that I can control my results. I have confronted my findings with some theoretical facts that have to be obeyed, and they do obey...( I off course need to know which Basis Set is used...) So if anybody could fax me a result, or if anybody has a reference to an article in which the atom-atom splittimgs are proposed, I would be very grateful if she/he could inform me on this matter... P.S. when I have studied the whole FORTRAN book I will try to change the 1993 version in the right way (namely through the FORTRAN code of GAMESS(US)). Any help is mighty welcome, Regards, |-----------------------------------------------------------------------| | C-C Patrick Bultinck | | / \ Dept. Physical & Inorganic Chemistry | | C-O O-C Section Quantum Chemistry | | | | University of Ghent | | C-O O-C Krijgslaan 281 (S-3) | | \ / 9000 Gent | | C-C Belgium | | Tel. Int'l code/32/9/264.44.44 | | Macrocycles Fax. Int'l code/32/9/264.49.83 | | Quantum Chemical E-mail : Patrick.Bultinck@rug.ac.be | | Calculations | |-----------------------------------------------------------------------| From ravishan@swan.wcc.wesleyan.edu Mon Apr 25 09:31:24 1994 Received: from swan.wcc.wesleyan.edu for ravishan@swan.wcc.wesleyan.edu by www.ccl.net (8.6.4/930601.1506) id IAA15421; Mon, 25 Apr 1994 08:52:12 -0400 Received: by swan.wcc.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA15544; Mon, 25 Apr 1994 08:48:52 -0400 Date: Mon, 25 Apr 1994 08:48:52 -0400 Message-Id: <9404251248.AA15544@swan.wcc.wesleyan.edu> From: "G. Ravishanker" To: vkitzing@sunny.mpimf-Heidelberg.mpg.de Cc: iyengar@qtp.ufl.edu, CHEMISTRY@ccl.net In-Reply-To: <9404251108.AA22991@sunny.mpimf-Heidelberg.mpg.de> (vkitzing@sunny.mpimf-Heidelberg.mpg.de) Subject: Re: CCL:helix dipole Hi If you have a set of charges qi, on atomic centers (xi,yi,zi), for i=1,natom, isn't it simpler to transform the coordinates to the principal axis system and do: dx = sum over all atoms qi*xi dy = sum over all atoms qi*yi dz = sum over all atoms qi*zi D = sqrt(dx**2 + dy**2 + dz**2) Ravi **************************************************************************** * Ganesan Ravishanker Ph: (203) 344-8544 Ext. 3110 * * Coordinator of Scientific Computing, Fax:(203) 344-7960 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wcc.wesleyan.edu * * Middletown, CT 06459. * **************************************************************************** From scsupham@reading.ac.uk Mon Apr 25 09:38:38 1994 Received: from mail2.rdg.ac.uk for scsupham@reading.ac.uk by www.ccl.net (8.6.4/930601.1506) id IAA15382; Mon, 25 Apr 1994 08:48:10 -0400 From: Received: from reading.ac.uk by mail2.reading.ac.uk with SMTP - Local (PP) id <04111-0@mail2.reading.ac.uk>; Mon, 25 Apr 1994 13:47:35 +0100 Date: Mon, 25 Apr 94 13:47:31 BST Message-Id: <1755.9404251247@scsscsc3> To: chemistry@ccl.net Subject: PostDoctoral Research Fellowship available Cc: scsupham@reading.ac.uk, M.G.B.Drew@reading.ac.uk Content-Type: X-sun-attachment ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 35 Hi, I am posting this job advertisement for a colleague: cut here--- I am looking for applicants for the following position. Enquiries on e-mail to scsdrew@reading.uk.ac phone 0734-875123 ex 7427 or send cv to Mike Drew, Department of Chemistry, University of Reading RG6 2AD University of Reading, Department of Chemistry Postdoctoral Research Fellowship. Computer Modelling Study of the Adsorption and Diffusion of Gases in Metal Oxides. Applications are invited for a postdoctoral fellowship funded by A.W.E.(plc) to study the adsorption and diffusion of gases in metal oxides by a variety of computer modelling techniques. Candidates should have a background in physical science and/or computing. The post is suitable for recent PhD graduates and is available for a year in the first instance, starting immediately. John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: job.ad X-Sun-Content-Lines: 27 I am looking for applicants for the following position. Enquiries on e-mail to scsdrew@reading.uk.ac phone 0734-875123 ex 7427 or send cv to Mike Drew, Department of Chemistry, University of Reading RG6 2AD University of Reading, Department of Chemistry Postdoctoral Research Fellowship. Computer Modelling Study of the Adsorption and Diffusion of Gases in Metal Oxides. Applications are invited for a postdoctoral fellowship funded by A.W.E.(plc) to study the adsorption and diffusion of gases in metal oxides by a variety of computer modelling techniques. Candidates should have a background in physical science and/or computing. The post is suitable for recent PhD graduates and is available for a year in the first instance, starting immediately. ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: .signature X-Sun-Content-Lines: 3 John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 From JKONG@ac.dal.ca Mon Apr 25 10:31:23 1994 Received: from SYSWRK.UCIS.DAL.CA for JKONG@ac.dal.ca by www.ccl.net (8.6.4/930601.1506) id JAA15880; Mon, 25 Apr 1994 09:35:22 -0400 Received: from AC.Dal.Ca by SYSWRK.UCIS.DAL.CA (PMDF V4.2-14 #2545) id <01HBL7SAFPGW005K6D@SYSWRK.UCIS.DAL.CA>; Mon, 25 Apr 1994 10:35:13 -0400 Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.2-14 #2545) id <01HBL6MYZCJ400KYOA@AC.DAL.CA>; Mon, 25 Apr 1994 10:35:02 -0300 Date: Mon, 25 Apr 1994 10:35:02 -0300 From: JING KONG Subject: Programs on coordinates To: chemistry@ccl.net Message-id: <01HBL6MZ0ORM00KYOA@AC.DAL.CA> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, I need a routine which can translate torsion angles into cartisian coordinates. The user does not need to input bond lengths and bond angles. The program should be able to estimate them. It should look like a molecular builder in the sence that it can put together the fragments with fixed bond lengths and bond angles, but take torsion angles as variables. I would imagine that there exists this kind of routine for some specific categories of molecule such as proteins and DNA. My question is wether there exists such routine for a general organic molecule? What about availability? Thank you in advance! Jing Kong Dalhousie From boehm@mulliken.cem.msu.edu Mon Apr 25 12:31:38 1994 Received: from msu.edu for boehm@mulliken.cem.msu.edu by www.ccl.net (8.6.4/930601.1506) id LAA18433; Mon, 25 Apr 1994 11:51:58 -0400 Received: from mulliken.cem.msu.edu by msu.edu (IBM VM SMTP V2R2) with TCP; Mon, 25 Apr 94 11:52:05 EDT Received: by mulliken.cem.msu.edu (920330.SGI/911001.SGI) for @msu.edu:CHEMISTRY@ccl.net id AA12233; Mon, 25 Apr 94 11:51:38 -0400 Date: Mon, 25 Apr 94 11:51:38 -0400 From: boehm@mulliken.cem.msu.edu (Randy Boehm) Message-Id: <9404251551.AA12233@mulliken.cem.msu.edu> To: CHEMISTRY@ccl.net Subject: lapack Dear Netters I am hoping that someone on this list will be able to help me. I've recently pulled a routine (DGELS) from lapack, formerly eispack, which is suposed to do a general linear least squares fit. However, when "netlib" sends a routine to me it sends only 1 routine at a time. Working on a piece by piece basis I have been able to retrieve a total of 21 routines that are called by the DGELS package, but there are at least 10 more routines that I have not been able to retrieve--that is netlib won't send them. Can anyone tell me where I can get ahold of the LAPACK routines: dlamc2 dtrsm dtrmm dtrmv dgemm dgemv dcopy dger dscal dnrm2 The first 9 on the list are subroutines and dnrm2 is a function. Many Thanks in advance, Randall C. Boehm, Scientist Michigan State Univerity COMMOC From rs0thp@RohmHaas.Com Mon Apr 25 13:31:33 1994 Received: from monte.br.RohmHaas.Com for rs0thp@RohmHaas.Com by www.ccl.net (8.6.4/930601.1506) id NAA19338; Mon, 25 Apr 1994 13:04:32 -0400 Received: by monte.br.RohmHaas.Com (AIX 3.2/UCB 5.64/4.03) id AA14934; Mon, 25 Apr 1994 13:03:25 -0400 From: rs0thp@RohmHaas.Com (Dr. Tom Pierce) Message-Id: <9404251703.AA14934@monte.br.RohmHaas.Com> Subject: Re: CCL:lapack To: boehm@mulliken.cem.msu.edu (Randy Boehm) Date: Mon, 25 Apr 1994 13:03:25 +22305458 (EDT) Cc: chemistry@ccl.net In-Reply-To: <9404251551.AA12233@mulliken.cem.msu.edu> from "Randy Boehm" at Apr 25, 94 11:51:38 am X-Mailer: ELM [version 2.4 PL13] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1043 Previously, Randy Boehm wrote: > I am hoping that someone on this list will be able to help me. > I've recently pulled a routine (DGELS) from lapack, formerly eispack, > which is suposed to do a general linear least squares fit. However, > when "netlib" sends a routine to me it sends only 1 routine at a time. > > Working on a piece by piece basis I have been able to retrieve > a total of 21 routines that are called by the DGELS package, but > there are at least 10 more routines that I have not been able to > retrieve--that is netlib won't send them. The easiest interface to netlib is xnetlib, an X-windows interface that allows you to select all dependent routines interactively. And then copy them locally with a single command. Without this package, I imagine that you will have to get the routines one-at-a-time or request netlib to mail you all of LAPACK. -- Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." From herbert.homeier@rchs1.chemie.uni-regensburg.de Mon Apr 25 14:31:34 1994 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.4/930601.1506) id NAA19755; Mon, 25 Apr 1994 13:41:59 -0400 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA07589 (5.65c/IDA-1.4.4 for ); Mon, 25 Apr 1994 19:41:53 +0200 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA08634; Mon, 25 Apr 94 19:40:49 +0200 Date: Mon, 25 Apr 94 19:40:49 +0200 From: Herbert Homeier (t4720) Message-Id: <9404251740.AA08634@rchs1.chemie.uni-regensburg.de> To: boehm@mulliken.cem.msu.edu Subject: Re: CCL:lapack Cc: CHEMISTRY@ccl.net Reply-To: Herbert.Homeier@chemie.uni-regensburg.de Return-Receipt-To: Herbert.Homeier@chemie.uni-regensburg.de Randall, Try to get the program xnetlib (running on unix work stations under X11). It can be found using archie. According to information on lapack under xnetlib, the following holds: For xnetlib users only, there is available a file "lapack/lapack.tar.Z" which is claimed to contain the complete package as a tar compressed file. I did not check, however, whether the sources that you miss are really included. Best regards Herbert -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: herbert.homeier@chemie.uni-regensburg.de (preferred) homeier@vax1.rz.uni-regensburg.d400.de na.hhomeier@na-net.ornl.gov -------------------------------------------------------------- ----- Begin Included Message ----- From chemistry-request@ccl.net Mon Apr 25 19:12:30 1994 To: CHEMISTRY@ccl.net Subject: CCL:lapack Sender: chemistry-request@ccl.net Content-Length: 1164 X-Lines: 42 Dear Netters I am hoping that someone on this list will be able to help me. I've recently pulled a routine (DGELS) from lapack, formerly eispack, which is suposed to do a general linear least squares fit. However, when "netlib" sends a routine to me it sends only 1 routine at a time. Working on a piece by piece basis I have been able to retrieve a total of 21 routines that are called by the DGELS package, but there are at least 10 more routines that I have not been able to retrieve--that is netlib won't send them. Can anyone tell me where I can get ahold of the LAPACK routines: dlamc2 dtrsm dtrmm dtrmv dgemm dgemv dcopy dger dscal dnrm2 The first 9 on the list are subroutines and dnrm2 is a function. Many Thanks in advance, Randall C. Boehm, Scientist Michigan State Univerity COMMOC ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net (port 70 or 73) Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search ----- End Included Message ----- From iyengar@qtp.ufl.edu Mon Apr 25 15:31:31 1994 Received: from crunch for iyengar@qtp.ufl.edu by www.ccl.net (8.6.4/930601.1506) id OAA20555; Mon, 25 Apr 1994 14:49:47 -0400 Received: by crunch (5.0/4.11) id AA02274; Mon, 25 Apr 1994 14:49:36 +0500 Date: Mon, 25 Apr 1994 14:49:36 +0500 From: "Srinivasan S. Iyengar" Message-Id: <9404251849.AA02274@crunch> To: vkitzing@sunny.mpimf-heidelberg.mpg.de Subject: Re: CCL:helix dipole Cc: CHEMISTRY@ccl.net, ravishan@swan.wcc.wesleyan.edu Content-Length: 386 > In his mail Eberhard von Kitzing says : > > As long as the helix is electrically neutral both results should agree! What if the number of positive charge centers is not equal to the number of negative charge centers. As for Ravi's idea of finding the principal axis, I donot quite understand how this helps simplify the problem. An explanation would be appreciated. Srinivasan From szeinfel@fox.cce.usp.br Mon Apr 25 15:38:04 1994 Received: from bee08.uspnet.usp.br for szeinfel@fox.cce.usp.br by www.ccl.net (8.6.4/930601.1506) id PAA20889; Mon, 25 Apr 1994 15:10:12 -0400 Received: from fox.cce.usp.br (fox.cce.usp.br [143.107.70.1]) by bee08.uspnet.usp.br (8.6.8.1/RISC-CCE2.0) id QAA29941 Received: from localhost (szeinfel@localhost) by fox.cce.usp.br (8.6.4/CONVEX120-CCE2.0) id QAA01894 Date: Mon, 25 Apr 1994 16:06:24 -0300 (BDT) From: Rafael N Szeinfeld Subject: Re: CCL:helix dipole To: "Srinivasan S. Iyengar" cc: chemistry@ccl.net In-Reply-To: <9404222014.AA04686@crunch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 22 Apr 1994, Srinivasan S. Iyengar wrote: > > In his mail Rafael Najmanovich says : > > > > For each pair of opposite charges in the helix you have a dipole > > momentum vector that points from the positive to the negative charge so I > > suppose the total dipole momenta vector of that helix will be the > > vectorial sum of all these vectors. How to calculate it in practice (that > > is, if there are approximation methods or computer algorhitms) I don't know. > > > > I beg to differ. I would rather - > (a) Find the center of mass of all the positive charges. > (b) Find the center of mass of all the negative charges. > (c) Find the dipole moment between these two points. > > Srinivasan Iyengar > I'm not sure but I think you'll problably get the same resultant vector. Rafael najmanovich From dbernhol@galilee.physique.usherb.ca Mon Apr 25 15:44:32 1994 Received: from galilee.physique.usherb.ca for dbernhol@galilee.physique.usherb.ca by www.ccl.net (8.6.4/930601.1506) id OAA20517; Mon, 25 Apr 1994 14:47:19 -0400 Received: by galilee.physique.usherb.ca (AIX 3.2/UCB 5.64/4.03) id AA22761; Mon, 25 Apr 1994 14:47:32 -0400 Message-Id: <9404251847.AA22761@galilee.physique.usherb.ca> From: de_bernholdt@fermi.pnl.gov (David E. Bernholdt) Date: Mon, 25 Apr 1994 14:47:27 -0400 In-Reply-To: rs0thp@RohmHaas.Com "CCL:lapack" (Apr 25, 1:03pm) X-Mailer: Mail User's Shell (7.2.5 10/14/92) To: rs0thp@RohmHaas.Com Subject: Re: CCL:lapack Cc: chemistry@ccl.net While Thomas Pierce is right about xnetlib being the simplest interface to netlib, the netlib mail server normally sends the routine requested _and_ its dependents. This behavior is "switched off" by using "send only" instead of "send". The "problem" here is different. LAPACK, like its predecessors LINPACK and EISPACK, are built on top of the BLAS (Basic Linear Algebra Subprograms). This is a separate library, also available on netlib (in source form), as well as from many vendors in the form of an optimized library. All but one of the routines Randy Boehm needs is in BLAS. The other is probably an LAPACK support routine which may well be packaged in a different subdirectory of the LAPACK hierarchy from the "working" routines. I believe this is covered in the documentation available with LAPACK. -- David E. Bernholdt | Email: de_bernholdt@fermi.pnl.gov Molecular Science Research Center | Phone: 509 375 4387 Pacific Northwest Laboratory, P.O.B. 999 | Fax: 509 375 6631 Richland, WA 99352-0999 | From julio@iqm.unicamp.br Mon Apr 25 16:32:22 1994 Received: from nyx.iqm.unicamp.br for julio@iqm.unicamp.br by www.ccl.net (8.6.4/930601.1506) id QAA26942; Mon, 25 Apr 1994 16:20:48 -0400 Received: (julio@localhost) by nyx.iqm.unicamp.br (8.6.8/8.3) id RAA17557; Mon, 25 Apr 1994 17:14:35 -0300 From: Julio Trevas Message-Id: <199404252014.RAA17557@nyx.iqm.unicamp.br> Subject: CCL:lapack To: CHEMISTRY@ccl.net Date: Mon, 25 Apr 1994 17:14:34 -0300 (EST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1062 Boehm, those routines are on the core library. Send an eletronic mail (to "netlib@research.att.com") message containing the line: send index from core Sincerely, Julio Trevas ************************************************************ * Julio Murilo Trevas dos Santos * * Depto. Fisico-Quimica - Instituto de Quimica * * Universidade Estadual de Campinas ( UNICAMP ) * * P.O. Box 6068 , 13083-970 Campinas, SP, Brasil * * e-mail: julio@iqm.unicamp.br * fax: (0055)(0192)393805 * ************************************************************ * "ANY PRACTICAL APPLICATION OF * * PHYSICS OBVIOUSLY INVOLVES MATTER, * * AND IS THEREFORE CHEMISTRY." * * Barry E. Rowe * ************************************************************ From elewars@alchemy.chem.utoronto.ca Mon Apr 25 17:32:47 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id RAA00332; Mon, 25 Apr 1994 17:27:23 -0400 Received: from localhost (elewars@localhost) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) id RAA03917 for chemistry@ccl.net; Mon, 25 Apr 1994 17:26:52 -0400 Date: Mon, 25 Apr 1994 17:26:52 -0400 From: "E. Lewars" Message-Id: <199404252126.RAA03917@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: MM and diastereomers Matthew Stahl asked if MM can be used to calculate the relative energies of diastreomers. In principle yes, for diastereomers (unlike enantiomers) are essentially just ordinary isomers. The problem is that they often differ only slightly in energy. Here are somesample results: FMeHC-CFMeH,meso diastereomer, C-F/C-Me anti conformer (A) vs threo diast, C-F/C-Me anti conf (B): MM2 A, 0.09 kJ B, 0 kJ (RELATIVE E's) AM1 A, 0.2 kJ B, 0 3-21G A, -5.59 kJ B, 0 For Z- and E- (i.e cis and trans) 1,2-diFethene (E/Z isomers are diastereomers too): MM2 Z, -5.10 kJ E, 0 AM1 Z, 0.0 kJ E, 0.0 kJ (sic) 3-21G Z, 5.88 kJ E, 0 6-31G* Z, 1.13 kJ E, 0 ==== As with any calc, the only way to be confident you can trust your results is to see how well analogous cases match experiment. === From rgab@purisima.molres.org Mon Apr 25 17:34:54 1994 Received: from purisima.molres.org for rgab@purisima.molres.org by www.ccl.net (8.6.4/930601.1506) id RAA00356; Mon, 25 Apr 1994 17:29:14 -0400 Message-Id: <199404252129.RAA00356@www.ccl.net> Received: by purisima.molres.org (1.37.109.4/16.2) id AA00505; Mon, 25 Apr 94 14:09:34 -0700 Date: Mon, 25 Apr 94 14:09:34 -0700 From: "R.G.A. Bone" To: chemistry@ccl.net Subject: diastereomers or enantiomers - THE ANSWER On the question of comparing the energies of "diastereomers", I followed the few publicly-posted answers and then the subsequent summary by Matthew Stahl. Although this discussion is now several days old, I believe that there is something else to contribute; I do not usually post answers publically but in this case I think there would be interest. Let us be very careful: Suppose that our molecule has a single asymmetric centre; if we invert at that centre and obtain the "enantiomer", then we have an energetically equivalent structure. That much we are all agreed upon. This should hopefully be irrespective of the force-field. One hopes that the Hamiltonian is symmetric w.r.t. inversion of all particle coordinates [(x,y,z,) -> (-x,-y,-z)] and in any case, as has been pointed out, this operation preserves inter-particle distances. [By way of an aside, although the traditional way of obtaining an enantiomer, is to 'reflect' in a plane, as is well known, a reflection operation is the composite of inversion through a center and a 2-fold rotation - neither of which alter the energy.] But, what happens if 2 chiral centres are present? (One may refer to a standard text-book of organic chemistry, e.g., March, if one is not familiar with the terms enantiomer and 'diastereomer'.) There are 4 possible isomers (assuming that the two centres do not contain identical sets of substituents). Now, let us write them schematically: V V V V | | | | U-C-W W-C-U U-C-W W-C-U | | | | X-C-Z Z-C-X Z-C-X X-C-Z | | | | Y Y Y Y A A' B B' Note that A and A' are enantiomers, as are B and B'. But the relationship of, say, A and B, is that they are diastereomers. "diastereomers are stereoisomers which are not enantiomers." For all 4 of these structures, the 'bonded' interactions are the same, and on that basis they will have identical energies. But it is the non-bonded interactions which discriminate. Note that the molecules A and A', in the configurations shown all have V---Y, W---Z and U---X _non-bonded_ interactions, whereas the pair B and B' have V---Y, U---Z and W---X non-bonded matches. (You can 'rotate' each of the C(XYZ) or C(UVW) centres but you can't get the same set of triple pair-wise interactions.) It is thus to be expected that the relative energies of diastereomers will depend upon the nature of the force-field used. Thus a very crude model, which does not contain the longer-range, non-bonded interactions will not distinguish energetically between diastereomers. The message is thus that, when more than one chiral centre is present, inversion at a single centre introduces changes in long-range pair-wise interactions which may well bea manifested in changes in the potential energy. Richard Bone ================================================================================ R. G. A. Bone. Molecular Research Institute, 845 Page Mill Road, Palo Alto, CA 94304-1011, U.S.A. Tel. +1 (415) 424 9924 x110 FAX +1 (415) 424 9501 E-mail rgab@purisima.molres.org From L338%SUEARN2.BITNET@mps.ohio-state.edu Mon Apr 25 17:32:44 1994 Received: from ohstpw.mps.ohio-state.edu for L338%SUEARN2.BITNET@mps.ohio-state.edu by www.ccl.net (8.6.4/930601.1506) id QAA28389; Mon, 25 Apr 1994 16:55:05 -0400 From: Received: from SUEARN2.BITNET (MAILER@SUEARN2) by MPS.OHIO-STATE.EDU (PMDF V4.2-14 #5888) id <01HBLL24QRAO8WWL50@MPS.OHIO-STATE.EDU>; Mon, 25 Apr 1994 16:55:00 EDT Date: Mon, 25 Apr 94 22:44 MSK Subject: Re:Ethylen calculation with GAMESS To: CHEMISTRY@ccl.net Message-id: <01HBLL24R0YA8WWL50@MPS.OHIO-STATE.EDU> Content-transfer-encoding: 7BIT > We are not able tlo create a z-Matrix for Ethylen. That is possible preparation of your data: 1. Write 'COORD=ZMT' keyword in $CONTR group. 2. Give full z-Matrix ( all atoms, not only symmetry unique ) in your $DATA group. From javito@netcom.com Mon Apr 25 18:31:28 1994 Received: from netcom.com for javito@netcom.com by www.ccl.net (8.6.4/930601.1506) id RAA00821; Mon, 25 Apr 1994 17:54:44 -0400 Received: by netcom.com (8.6.8.1/SMI-4.1/Netcom) id OAA06799; Mon, 25 Apr 1994 14:55:42 -0700 From: javito@netcom.com (James Vito) Message-Id: <199404252155.OAA06799@netcom.com> Subject: z-matrix -> coordinates To: chemistry@ccl.net Date: Mon, 25 Apr 1994 14:55:38 -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: 202 I am looking for an application to convert a z-matrix -> cartesian coordinates. The source code in C or Pascal would be very convenient. If not an application... maybe an algorithm. Thanks. Jim Vito From GKING@arserrc.gov Mon Apr 25 18:34:01 1994 Received: from arserrc.gov for GKING@arserrc.gov by www.ccl.net (8.6.4/930601.1506) id SAA00962; Mon, 25 Apr 1994 18:29:39 -0400 From: Received: from arserrc.gov by arserrc.gov (PMDF V4.2-11 #2923) id <01HBLOD8KC34000CT5@arserrc.gov>; Mon, 25 Apr 1994 18:29:38 EDT Date: Mon, 25 Apr 1994 18:29:37 -0400 (EDT) Subject: CCL:helix dipole To: chemistry@ccl.net Message-id: <01HBLOD8L50Y000CT5@arserrc.gov> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT >On Fri, 22 Apr 1994, Srinivasan S. Iyengar wrote: > >> >>In his mail Rafael Najmanovich says : >>> >>> For each pair of opposite charges in the helix you have a dipole >>> momentum vector that points from the positive to the negative charge so I >>> suppose the total dipole momenta vector of that helix will be the >>> vectorial sum of all these vectors. How to calculate it in practice (that >>> is, if there are approximation methods or computer algorhitms) I don't know. >>> >> >> I beg to differ. I would rather - >> (a) Find the center of mass of all the positive charges. >> (b) Find the center of mass of all the negative charges. >> (c) Find the dipole moment between these two points. >> >> Srinivasan Iyengar >> > I'm not sure but I think you'll problably get the same resultant >vector. > > Rafael najmanovich As was noted by a previous poster, the definition of the dipole moment vector is: mu_x = SUM_i q_i * (x_i - x0) mu_y = SUM_i q_i * (y_i - y0) mu_z = SUM_i q_i * (z_i - z0) where mu_x, mu_y, mu_z are the components of the dipole moment vector mu along the x, y, z axes (respectively); q_i is the charge of entity i; x_i, y_i, z_i are the cartesian coordinates of entity i; and x0, y0, z0 are the cartesian coordinates of a reference point. For electrically neutral molecules mu is independent of the reference point. Otherwise the molecule's center of mass is conventionally used as (x0,y0,z0). The molecule's principle axes provide three convenient orthogonal vectors that may be used to define the x, y, and z axes. The equations above are the correct ones to use, and are just as easy (if not easier) to program than some of the schemes provided by other posters (I assume the original poster did not want to do these calculations by hand). ==================================================================== Gregory King Internet: gking@arserrc.gov Eastern Reg. Res. Ctr., ARS, USDA Voice: (1) 215 233 6675 600 East Mermaid Lane Fax: (1) 215 233 6559 Philadelphia, PA 19118-2551 ==================================================================== From tropsha@gibbs.oit.unc.edu Mon Apr 25 21:31:30 1994 Received: from gibbs.oit.unc.edu for tropsha@gibbs.oit.unc.edu by www.ccl.net (8.6.4/930601.1506) id UAA02051; Mon, 25 Apr 1994 20:47:31 -0400 Received: by gibbs.oit.unc.edu (5.64/10.1) id AA22665; Mon, 25 Apr 94 20:47:29 -0400 Date: Mon, 25 Apr 1994 20:47:27 -0400 (EDT) From: Alex Tropsha Subject: acethylcholine To: CCL Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters: Does anyone have macromolecular forcefield parameters (e.g., AMBER, GROMOS, CHARMm) for acethylcholine? Please respond directly to me. Thank you. Alexander Tropsha, Ph.D. Assistant Professor, Director the Laboratory for Molecular Modeling CB # 7360, Beard Hall School of Pharmacy University of North Carolina Chapel Hill, NC 27599-7360 Tel. (919) 966-2955 Fax (919) 966-6919