From chemistry-request@www.ccl.net Wed Sep 23 03:26:28 1998 Received: from hpserv.imim.es ([193.144.6.104]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA25984 Wed, 23 Sep 1998 03:26:26 -0400 (EDT) Received: from i25.imim.es ([193.144.6.234]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3) id SN0KRG20; Wed, 23 Sep 1998 09:24:34 +0100 Message-ID: <3608A289.C78A6D2F@imim.es> Date: Wed, 23 Sep 1998 09:26:01 +0200 From: "Jordi Villŕ" X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: MEPSIM 2.4 X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit MEPSIM (http://www1.imim.es/~mepsim/index.htm) is a computational system developed by the Department of Medical Computer Sciences of the Institut Municipal d'Investigació Mčdica of Barcelona.(1) It permits an integrated computation and analysis of the Molecular Electrostatic Potential (MEP). It includes the following main modules: MEPMIN: A module which allows to find automatically the MEP minima of a molecular system. It supplies the cartesian coordinates of these minima, their values and all the geometrical relationships between them (distances, angles and dihedral angles). This module uses the exact definition of MEP.(2) MEPCOMP: This module computes a similarity coefficient between the MEP distributions of two molecules and finds their relative position that maximizes this electrostatic similarity.(3,4) In MEPSIM 2.4 there is a new utility that allows the comparison of the whole MEP distributions of two molecules or only their negative zones.(5) The second option avoids the influence of the nuclear positive MEP zones in the comparison. In this option the user can define the MEP value that limits the negative MEP zones to be considered. An earlier version of MEPSIM, that was programmed to run on a VAX system, included other modules. The migration of VAX systems to UNIX workstations in many research laboratories, made convenient to develop a new version of the MEPSIM package that runs on UNIX SGI machines. Nevertheless some options of the package have not yet been completely developed for UNIX SGI systems, so they are not available in this new version of MEPSIM. On the other side, the capabilities of the available modules in terms of maximum number of atoms and orbitals, have been increased. 1.Sanz F, Manaut F, Rodriguez J, Lozoya E, and López-de-Brinas E, MEPSIM: A computational package for analysis and comparison of moleculra electrostatic potentials. J. Comput.-Aided Mol. Design, 7(1993)337. 2.Sanz F, Manaut F, José J, Segura J, Carbó M and De-la-Torre R, Automatic determination of MEP patterns of molecules and its application to cafeine metabolism inhibitors. J. Mol. Struct. (Theochem) 170(1988)171. 3.Sanz F, Manaut F, José J and Milesi M, Automatic search for maximun similarity between molecular electrostatic potential distributions. J. Comput.-Aided Mol. Design, 5(1991)371. 4.Manaut F, Lozoya E and Sanz F, Automatic determination of maximun electrostatic alingment between methotrexate and dihydrofolic acid. In Silipo,C. and Victoria, A. (Eds) QSAR: Rational Aproaches to the Design of Bioactive Compounds, Elsevier, Amsterdam, 1991, pp. 339-342. 5.Lozoya E, Berges M, Rodriguez J, Sanz F, Loza MI, Moldes VM, Masaguer CF Comparison of electrostatic similarity approaches applied to a series of ketanserin analogues with 5-HT2A antagonistic activity. Quant Struc-Act Relat, 17(1998)199. -- Jordi Villŕ Research Group on Medical Informatics Carrer del Doctor Aiguader 80 E-08003 Barcelona Tlf: 34-93-2211009 Fax: 34-93-2213237 jvilla@imim.es From chemistry-request@www.ccl.net Wed Sep 23 03:46:26 1998 Received: from apollon.bender.co.at (apollon.bender.co.at [193.154.107.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA26058 Wed, 23 Sep 1998 03:46:22 -0400 (EDT) Received: from vieexch1.vie.at.bic (vieexch1 [148.190.11.2]) by apollon.bender.co.at (8.9.1/8.6.9) with ESMTP id JAA00204 for ; Wed, 23 Sep 1998 09:46:19 +0200 Received: by vieexch1.vie.at.bic with Internet Mail Service (5.5.1960.3) id ; Wed, 23 Sep 1998 09:39:59 +0200 Message-ID: <4195A3C6D39BD11189C30020AFFC17588F3BD9@vieexch1.vie.at.bic> From: "LOEFFLER,DR,GERALD FEM BENAT" To: chemistry@www.ccl.net Subject: RE: CASP vs. The Tower of Babel Date: Wed, 23 Sep 1998 09:39:58 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Content-Type: text/plain; charset="iso-8859-1" Hi! So why is there no collaboration on the code-level between computational scientists? I don't want to over-simplify the problem, but one important reason IMHO is the fact that traditionally computational scientists have been _lousy_ programmers. While the technology to make interoperable application components has been there for some time (I'm particularly thinking of OO technology), computational scientists have been too inexperienced in software engineering techniques to exploit this technology. As a concrete example: It would be almost trivial to design an OO framework for Energy Minimization (or Molecular Dynamics or Threading, ...) where the force-field would be just one component that you "plug" into the framework. The same is true for such algorithmic components as minimization strategies, potentials of mean force, integration algorithms, Monte Carlo moves, Genetic Algorithms, etc. But is the resulting code efficient? It's certainly a lot slower than FORTRAN! (For language reasons and because you loose opportunities for source-level optimizations if components have to be truly independent of each other.) But I would argue that firstly speed of execution does not matter at this level (we are not talking about production code here). And secondly, on the other hand, of what use is speed of execution if you can not get the functionality you want (interoperability of algorithms, in this case) with reasonable effort? But things _are_ getting better: MMTK springs to my mind, and also the OMG effort to standardize interfaces for biological sequence analysis (although this is not an academic effort). And of course there are programs which are not designed with OO techniques and consequent interoperability in mind, but which are simply well written (TINKER, for instance). (Regarding unwillingness to give away source code at all: With Java you can even give away the "object code" (byte code) (maybe after running it through an obfuscator) and it will work on any Java platform...) cheers, gerald |--------------------------------------------------------------------| Gerald Loeffler - Bioinformatics Scientist Boehringer Ingelheim R&D Vienna Email: Gerald.Loeffler@vienna.at Phone: +43 676 3289588 (and +43 1 80105 634) Fax: +43 1 80105 683 Smail: Bender+Co, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria > -----Original Message----- > From: Gabriel Berriz [SMTP:berriz@potato.harvard.edu] > Sent: Sunday, September 20, 1998 7:53 PM > To: chemistry@www.ccl.net > Subject: CCL:CASP vs. The Tower of Babel > > > > I study the statistical mechanics of protein folding using minimal > computer models. I find that my specialty has a Tower of Babel > (Babble?) problem, and perhaps the same is true of the whole field of > computational protein studies, or even of all of computational > chemistry. It has to do with checking and building on the results of > others. I was an experimentalist in cellular immunology for a few > years before switching to my current field, and I recall that trading > reagents, libraries, strains, was quite common in that field. I often > unpacked little vials shipped in dry ice, and bearing some precious > mutant; typically, after some quick tests, I was up and running with > the new stuff. Not much was required from the source of the samples > (a couple of concentrations, buffers used, maybe some growth > conditions here and there...). > > *Nothing* like this happens in my current field. I'm not sure why, > but I have a few guesses. For one thing, programs are a pain to port > across systems (portability of code is not a criterion for > publication). More important, in most cases I don't want the program > just to use as a black box. On the contrary, my interest in the > program is usually in how it implements a model; I want not only to > reproduce published results, but also to tweak the conditions, and to > extend the experiments. This invariably requires that I understand > enough of the code to hack away in it, and here's where I hit the > biggest wall. It takes me too long to understand the code written by > my *labmates*, let alone that written by some unknown graduate student > 5 years ago half a world away. (Again, clarity of code is, for the > most part, not a criterion for publication). So, typically I conclude > that either I re-implement the idea from scratch, which is usually > something I can't afford, or else I drop the matter altogether. > (Incidentally, in the few cases I've tried to get source code from > other labs, I've received such unequivocal, resounding, unapologetic > refusals, that I must conclude my request was deemed to be bad > manners.) > > It is, in my opinion, a very serious problem; it reduces the field to > a collection of largely independent efforts, deprived of one of the > greatest strengths of the scientific method, namely, the ability to > test and build upon the work of others. I wonder if others feel > similarly. > > I think this frustrating situation was what ultimately gave rise to > the biennial structure prediction competition CASP (Critical > Assessment of techniques for protein Structure Prediction), in which > participants put their structure prediction programs through the fire > test of predicting some recently solved protein structures prior to > their publication. This skips over the problem of understanding the > programs and the models devised by others by focusing on "objective > results". Faced with this clear prize, the field has naturally > responded by a adopting an increasingly heuristic attitude: whatever > works, however ad hoc or poorly understood, throw it in there. If you > loose, no one will care, and if you hit the CASP jackpot, then > "there's no arguing with success!" > > Well, I guess that's *one* way to deal with our Tower of Babel > problem, but I wonder where this leaves the science... I'm relatively > new to this field, though, and I wonder what others with more > experience feel about these issues. > > Best wishes, > > Gabriel Berriz > Department of Chemistry and Chemical Biology > Harvard University > berriz@potato.harvard.edu > For best results, replace the word potato by chasma in my address. > > > --- > Administrivia: This message is automatically appended by the mail > exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: > Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: > www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive > search > Web: http://www.ccl.net/chemistry.html > --- From chemistry-request@www.ccl.net Wed Sep 23 08:36:29 1998 Received: from rs5.thch.uni-bonn.de (rs5.thch.uni-bonn.de [131.220.44.15]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA26988 Wed, 23 Sep 1998 08:36:26 -0400 (EDT) Received: (from bernd@localhost) by rs5.thch.uni-bonn.de (8.8.8/8.8.5) id OAA15662 for chemistry@www.ccl.net; Wed, 23 Sep 1998 14:36:54 +0200 From: Bernd Engels Message-Id: <199809231236.OAA15662@rs5.thch.uni-bonn.de> Subject: books for theor.chem. To: chemistry@www.ccl.net (Computational Chemistry List) Date: Wed, 23 Sep 1998 14:36:53 +0200 (MES) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hy, I would be interested in an overview about good books about Theoretical Chemistry. I am mainly interested in books for undergraduate students but other comments are also highly appreciated. Of course I will summarize Bernd Engels Inst. fuer Phys. und Theor. Chemie Universitaet Bonn Germany From chemistry-request@www.ccl.net Wed Sep 23 12:02:56 1998 Received: from sp2n17.missouri.edu (sp2n17-a.missouri.edu [128.206.3.17]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA28936 Wed, 23 Sep 1998 12:02:55 -0400 (EDT) Received: from math.missouri.edu (math.missouri.edu [128.206.72.13]) by sp2n17.missouri.edu (8.9.0/8.9.0) with SMTP id LAA148130 for <@sp2n17-t.missouri.edu:chemistry@www.ccl.net>; Wed, 23 Sep 1998 11:02:55 -0500 Received: from hamilton.math.missouri.edu by math.missouri.edu via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for <@math.missouri.edu:chemistry@www.ccl.net> id LAA09843; Wed, 23 Sep 1998 11:02:54 -0500 Received: by hamilton.math.missouri.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id LAA15476; Wed, 23 Sep 1998 11:02:53 -0500 From: "Don Steiger" Message-Id: <9809231102.ZM15474@hamilton.math.missouri.edu> Date: Wed, 23 Sep 1998 11:02:52 -0500 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: multi-time scale symplectic integration. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii I was wondering if somebody could point me to any papers where high order exponential decompositions are used for integrating classical Hamiltonian systems. I am curious as to how these methods perform in real life. -- Don Steiger dons@hamilton.math.missouri.edu From chemistry-request@www.ccl.net Wed Sep 23 15:07:25 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA11100 Wed, 23 Sep 1998 15:07:25 -0400 (EDT) Received: from mserv1.dl.ac.uk (root@mserv1.dl.ac.uk [148.79.160.65]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA25492 for ; Wed, 23 Sep 1998 15:07:21 -0400 (EDT) Received: from tcsi.dl.ac.uk (tcsi.dl.ac.uk [193.62.112.84]) by mserv1.dl.ac.uk with SMTP id UAA26858 (8.8.8/5.4[ref postmaster@dl.ac.uk] for dl.ac.uk from P.Sherwood@dl.ac.uk); Wed, 23 Sep 1998 20:07:21 +0100 (BST) Precedence: first-class Received: by tcsi.dl.ac.uk (SMI-8.6/SMI-SVR4) id UAA22507; Wed, 23 Sep 1998 20:08:24 +0100 Date: Wed, 23 Sep 1998 20:08:24 +0100 From: P.Sherwood@dl.ac.uk (P. Sherwood) Message-Id: <199809231908.UAA22507@tcsi.dl.ac.uk> To: chemistry@ccl.net Subject: Announcement: CCP1 Study Weekend on Ab Initio Molecular Dynamics X-Sun-Charset: US-ASCII UK Collaborative Computational Project (CCP) 1 Study Weekend Ab Initio Molecular Dynamics ============================ 30 October - 1 Nov 1998 at CLRC Daresbury Laboratory Warrington, WA4 4AD, UK Scope ***** The basic principle of ab initio Molecular Dynamics is the use of dynamics with an "on the fly" evaluation of the gradient. In addition, this method is often coupled with the propagation of the wavefunction using quasi-Newtonian or Schroedinger equations of motion. The Car-Parinello method is beginning to be used in quantum chemistry applications and is most commonly applied in the context of DFT with plane waves. To a quantum chemist, ab initio Molecular Dynamics looks much like simultaneous wavefunction and geometry optimisation which can be efficient for large molecules. However, simulation of dynamics often gives new insights and is crucial for extended condensed systems such as liquids. Even though quantum chemistry techniques are capable of treating systems with increasing numbers of atoms, the application of dynamics methods is in quantum chemistry is still in its infancy. This study weekend brings together the established practitioners in the field >from the Car Parinello community, as well with those who are beginning to use such methods in traditional quantum chemistry. Programme ********* All speakers are requested to allow at least 15 min. for discussion. Fri 30 October Arrival: Accomodation at Daresbury Park Hotel and the Daresbury hostel Saturday 31 Oct, AM, Chairman Ian Hillier (Manchester) 08:30 ------ Registration at Daresbury Laboratory 09:00-09.05 M. A. Robb (King's College, London) Opening Remarks 09:05-10.05 M. Parrinello ( Max-Planck-Institut Stuttgart) Title to be announced 10:05-10:30 Coffee + Posters 10:30-11:30 Paul Madden (Oxford) Orbital-free density functionals in the AIMD simulation of metals 11:30-12:30 Michiel Sprik (Cambridge) Ab Initio Molecular Dynamics of Liquids and Solutions 12:45 ------- Lunch (Daresbury Laboratory) Saturday 31 Oct, PM, Chairman Nicholas Handy (Cambridge) 14:00-15:00 Berny Schlegel (Detroit) Ab initio classical trajectories on Born-Oppenheimer surfaces. Some aspects of hessian based integrators. 15:00-16:00 Todd Martinez (Illinois) Ab Initio Molecular Dynamics with Quantum Effects. 16:00-16:30 Tea + Posters Chairman Brian Sutcliffe (York) 16:30-17:30 Richard Bryce (Manchester) Cooperative Effects in Fluoride/Water Clusters 19:00 ------ Bar and Dinner will be at the Daresbury Park hotel Sunday 1 Nov, AM, Chairman M.A. Robb (King's College, London) 09:00-10.00 Thanh Truong (Utah) Quantum Modeling of Reactions at Solid-Gas and Solid-Liquid Interfaces 10:00-10:30 Coffee + Posters 10:30-11:30 Andrew Willetts (Cambridge) Direct Energy Minimisation 11:30-12:30 Mike Payne (Cambridge) Finite Temperature Simulations of Zeolites and Metallic Surfaces. 12:30 ----- Buffet Lunch at Daresbury Laboratory, departure. Registration and Practical Details *********************************** Two accomodation options are available, the prices include 2 nights accomodation, meals and transport between accomodation and the meeting, which will be held in the Merrison Lecture theatre at Daresbury Laboratory. 1) The Daresbury Park Hotel. Cost 205 pounds We have agreed a special rate for executive-class rooms at this local 4-star local hotel. 2) The Daresbury Laboratory Hostel Cost 85 pounds The Daresbury Hostel provides budget accomodation for users of the Synchrotron Radiation Source. The rooms are single occupancy with shared bathroom facilities. 3) No Accomodation option Cost 40 pounds A copy of this information, together with links to travel information and the registration form can be found on the CCP1 web page at http://www.dci.clrc.ac.uk/Activity/CCP1 In the event of any problems with this page, (there have been some teething troubles associated with recent changes to server) the study weekend information is also available at http://www.dl.ac.uk/TCSC/QuantumChem/ccp1sw.html. Please register using the on-line form, and send a cheque made payable to CLRC Daresbury Laboratory, to Mrs Shirley Miller, CLRC Daresbury Lab, Warrington WA4 4AD, UK. Poster presentations are welcome, contributors should send an abstract, (less than 1 page in length) with the remittance. A limited number of hotel and hostel rooms have been booked, and these will be assigned on a first-come, first-served basis. Early registration is advised, after 30th September availability of rooms and the rates given here cannot be guaranteed. Attendees should arrange to arrive directly at their accomodation on Friday evening, and can pick up copies of the programme for the meeting outside the Lecture Theatre on Saturday Morning. Further queries may be directed to p.sherwood@dl.ac.uk or s.miller@dl.ac.uk (local organisation) mike.robb@kcl.ac.uk and r.hall@man.ac.uk (scientific programme). From chemistry-request@www.ccl.net Wed Sep 23 19:12:43 1998 Received: from ns-mx.uiowa.edu (ns-mx.uiowa.edu [128.255.1.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA10664 Wed, 23 Sep 1998 19:12:42 -0400 (EDT) Received: from [128.255.138.237] (his.chem.uiowa.edu [128.255.138.237]) by ns-mx.uiowa.edu (8.8.8/8.8.5) with ESMTP id SAA54798 for ; Wed, 23 Sep 1998 18:12:45 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 23 Sep 1998 18:15:39 -0500 To: chemistry@www.ccl.net From: "Jan H. Jensen" Subject: EPR g-factors Hello, I am interested in calculating anisotropic EPR g-factors using ab initio electronic structure theory. I would like to know what programs can calculate this property, and what kind of accuracy one can expect. Best regards, Jan Jensen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Assistant Professor Department of Chemistry jan-jensen@uiowa.edu University of Iowa Phone:(319) 335-1108 Iowa City, IA 52242 FAX: (319) 335-1270 http://www.uiowa.edu/~chemdept/faculty/jensen/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@www.ccl.net Wed Sep 23 22:10:03 1998 Received: from avanti.nmsu.edu (avanti.NMSU.Edu [128.123.8.92]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA21271 Wed, 23 Sep 1998 22:10:02 -0400 (EDT) Received: (from abjones@localhost) by avanti.nmsu.edu (AIX4.2/UCB 8.7/8.7) id TAA18090; Wed, 23 Sep 1998 19:45:52 -0600 (MDT) Date: Wed, 23 Sep 1998 19:45:51 -0600 (MDT) From: Abraham Jones To: chemistry@www.ccl.net Subject: Contour Plots Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Greetings from NM. I found your address on the internet when I search for help on generating contour plots with Gnuplot . I'm trying to generate some 2-D contour plots and I can't get it to work. Gnuplot always says that it can't contour non-grid data. I have my data files set up with three columns x,y & z. I can contour them just fine with Sigma Plot and I don't understand why gnuplot doesn't take my data files. Any help would be welcome. Thanks Abraham Jones ajones@cs.nmsu.edu