From chemistry-request@server.ccl.net Wed Jan 31 18:42:01 2001 Received: from sundown.cs.cornell.edu (sundown.cs.cornell.edu [128.84.96.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0VNg1w08287 for ; Wed, 31 Jan 2001 18:42:01 -0500 Received: from fafe.cs.cornell.edu (IDENT:avijit@fafe.cs.cornell.edu [128.84.97.167]) by sundown.cs.cornell.edu (8.9.3/8.9.3/R-3.2) with ESMTP id SAA23849 for ; Wed, 31 Jan 2001 18:42:02 -0500 (EST) Date: Wed, 31 Jan 2001 18:42:02 -0500 (EST) From: Avijit Ghosh X-Sender: To: Subject: GPL'd MD packages In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I was wondering whether anyone has any GPL'd code for MD? Particularly, whether there are any GPL'd force field implementations out there (I.E. MM*/OPLS*/AMBER* ). Cornell U. has a package (MOIL) here that is more or less public domain which includes an Amber88/(soon to be 95 implementation). There are a series of very nice programs that are available with source (NAMD/VMD from UIUC), Tinker from wustl (which is a really nice package btw) but is definitely copyrighted. However the licensing on these doesn't really encourage code reuse rather just personal code modification, and it would seem to me that code reuse might be beneficial in some circumstances rather than everyone reimplementing everyone elses algorithms/methods/force fields. In any case i'm curious as to what is out there already if anything. -Avi (W/ apologies about fomenting the Fortran/C++ war into a source code licensing war :) ) Actually w/ regards to programming languages, let me mention that I did my undergrad. in CS and at the time we did every class (except for operating systems) in Pascal which isn't obviously "useful". Really, language doesn't matter; you can write equally crap/unmaintainable code in all! :) From chemistry-request@server.ccl.net Thu Feb 1 02:37:49 2001 Received: from gip.u-picardie.fr (gip.u-picardie.fr [193.49.184.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f117bmw11462 for ; Thu, 1 Feb 2001 02:37:48 -0500 Received: from labo5 (labo5.sa.u-picardie.fr [195.83.150.83]) by gip.u-picardie.fr (8.9.3/8.9.3) with SMTP id IAA18815; Thu, 1 Feb 2001 08:37:36 +0100 Date: Thu, 1 Feb 2001 08:37:36 +0100 Message-Id: <200102010737.IAA18815@gip.u-picardie.fr> X-Sender: fyd-phar@mailx.u-picardie.fr X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: amber@cgl.ucsf.EDU From: Francois Dupradeau Subject: SUMMARY for GAMESS/GAUSSIAN MEP Cc: chemistry@ccl.net Dear All, Few days ago, I asked questions about MEP obtained with GAMESS/GAUSSIAN : - Here, are the 3 answers I got : Best regards, Francois ________________________________________________ Return-Path: Date: Fri, 26 Jan 2001 15:10:44 +0100 To: Francois Dupradeau From: aldo jongejan Subject: Re: CCL:MEP with GAMESS or GAUSSIAN Actually, you should do a conformation search of the molecule, cluster the conformations according to some parameter (fx. distance between heteroatoms) select about 4 conformations (if possible) and calculate the ESP using GAMESS (single point calculations, 6-31G*). Then you have to convert the grid points using a script to make them suitable for input to RESP. RESP will then perform the fitting and give you partial charges. The partial charges are indeed conformation depended. If I remember correctly the script needed to convert the GAMESS-ESP output can be found at the AMBER-homepage. greetings, aldo ____________________________________________ Return-Path: From: "Bultinck, Patrick [JanBe Extern]" To: "'chemistry@ccl.net'" Subject: CCL:MEP with GAMESS or GAUSSIAN Date: Fri, 26 Jan 2001 16:55:13 +0100 Sender: "Computational Chemistry List" Errors-To: chemistry-request@ccl.net Different parameters may play a role : GAMESS keyword Gaussian keyword - Number of layers see LAYER in $PDC IOp(6/41) - Density of points on layer see PTDENS in $PDC IOp(6/42) - Increment between layers see VDWINC in $PDC IOp(6/43) - vdW scale factor for 1st layer see VDWSCL in $PDC IOp(6/56) but added this one myself :-) If you would take the points from GAMESS (standard provided by GAMESS), and insert them into G98, take care in symmetry, use NoSymm, I would say. Maybe using the same parameters in both programs, you might still want to check if the same points are being used on some surface (CONNOLLY). Gamess does this happily, G98 only if providing some overlay options (but again, added some myself for extra flexibility in G98). Also make a note what multipoles you are constraining in both molecules, just total charge, or dipole as well, or quadrupole maybe. You can almost perfectly reproduce things between the two programs (see also source file prplib.src of GAMESS where this is also mentionned), if you 'play' around with the options, making sure you are doing the same thing in both programs... Hope this might help a little (sorry for sending this to the entire list, I lost the original mail, and had this reply lying about, forgetting to send it. Maybe it is still of help to the original sender !) Kind regards, Patrick Bultinck _________________________________________________________ Return-Path: Date: Fri, 26 Jan 2001 12:32:44 -0500 From: "Curt M. Breneman" Reply-To: brenec@rpi.edu Organization: RPI Department of Chemistry To: Francois Dupradeau CC: amber@cgl.ucsf.edu, chemistry@ccl.net Subject: Re: CCL:MEP with GAMESS or GAUSSIAN References: <200101261216.NAA31906@gip.u-picardie.fr> Folks, This was the motivation for utilizing a higher point densities and using a different sampling strategy in the CHELPG routine that's implemented in Gaussian9x. See: Breneman, C.M. and Wiberg, K.B., "Determining Atom-Centered Monopoles > from Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis",J. Comp. Chem., 1990,11(3), p. 361-373. Curt Breneman RPI Chemistry _______________________________________________________________ -- F.-Y. Dupradeau http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/fyd.htm From chemistry-request@server.ccl.net Thu Feb 1 02:58:19 2001 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f117wIw11676 for ; Thu, 1 Feb 2001 02:58:18 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Thu, 1 Feb 2001 08:54:46 +0100 Message-ID: <003501c08c24$d3df1e20$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: "Ulrike Salzner" , References: Subject: Re: CCL:programming language Date: Thu, 1 Feb 2001 08:58:56 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f117wJw11677 It would be difficult to answer in one word. If more or less serious programming is concerned, C/C++. An easier entry is Visual Basic, it is more convenient for small tasks. On the other hand, if somebody has some basic knowledge of VB, the Visual Basic-based scripts and macros of World, Excel etc are within easy understanding and usage. Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Subject: CCL:programming language > > We are a chemistry department and our first year students take a computer > science cours learning JAVA. They told me that they don't think it is of > any use to them. > > I would like to collect opinions which programming language is most useful > for chemists. Let's assume they are learning only one. > > Thanks, > Ulrike Salzner > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Thu Feb 1 00:55:28 2001 Received: from hotmail.com (f11.law4.hotmail.com [216.33.149.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f115tRw10853 for ; Thu, 1 Feb 2001 00:55:27 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 31 Jan 2001 21:53:28 -0800 Received: from 134.172.64.22 by lw4fd.law4.hotmail.msn.com with HTTP; Thu, 01 Feb 2001 05:53:28 GMT X-Originating-IP: [134.172.64.22] From: "Douglas Smith`" To: chemistry@ccl.net Subject: programming language Date: Thu, 01 Feb 2001 00:53:28 -0500 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 01 Feb 2001 05:53:28.0513 (UTC) FILETIME=[4CAE4310:01C08C13] I am somewhat surprised to see how many people are suggesting FORTRAN. Perhaps this is due to the bias of this list, which is primarily focused on molecular modeling, theoretical chemistry, and high end number crunching. Perhaps it is due to the fact that so many of us have been around so long and historically, FORTRAN is where we came from and our first love. (In the same vein, Mark Zottola says almost 100% of the supercomputer codes at Alabama are FORTRAN... is this possibly historical? What about codes that have originated within the past few years rather than those that have been around for so long, like GAMESS, AMBER, etc.) Jan: what is the percentage makeup of codes at the Ohio Supercomputer Center? And, since OSC is still involved (I believe) with the computational chemistry codes at the DOD Major Shared Resource Centers, what is the makeup there? That would be of interest, since so many of those codes had to be rewritten (or newly developed) for the highly parallel machines at those centers? At the same time, I notice that we have not yet heard from commercial software developers, such as Gaussian Inc., Schrodinger, Tripos, or MSI. I believe that MSI is the largest "group" of PhD computational chemists in the world, and many of them read this list. What is the language used for commercial codes? Feel free to break down your analysis to discuss front ends separate from servers, and to even tell us the answer based on the type of codes. Now, what about all those other types of "computational chemistry" activities, such as cheminformatics? I know that RS3, Oxford Molecular's database/registration code, is written in C. What about other informatics codes? Also conspicuously absent so far is Henry Rzepa. Henry, if you are listening, I know you have an opinion. You have done some wonderful work on graphics and browser-based chemistry, what do you think? And yes, what about a language for those chemistry students that will not become computational or theoretical chemists? Isn't JAVA, or C++ or Visual Basic important to them, so that they can work with information exchange, build little applets and servlets that will ease their workflow in the labs? For that matter, what about LabView, Mathmatica, or other languages for interfacing equipment to computers, creating forms and documents and reports, and more? In the broader scheme of things, the best answer to the original question is that the language of most utility will depend on the student, their projects and type of work they do. Later in their professional lives, the same question would be answered by stating that it depends on their workflow and corporate environment. > From a pedagogical point of view (and I am not a programmer nor a computer scientist) what ever course can teach them strongly in the fundamentals of good code design and programming practices, starting from the proper time and effort spent on functional and engineering specifications, including key points such as the need for documenting code, good QA/QC, and even perhaps an introduction to the CMM levels would be good. If we teach fundamentals and good practices, careful thought and execution, any programming language should be useful. These opinions and comments are my own, not my company's... otherwise I would use their email system. :>) Doug Smith Product Manager, ADME/Tox software Oxford Molecular Group (a wholly owned subsidiary of Pharmacopeia) _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com From chemistry-request@server.ccl.net Thu Feb 1 04:09:26 2001 Received: from relay.unizar.es (aspe.unizar.es [155.210.3.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1199Pw12552 for ; Thu, 1 Feb 2001 04:09:25 -0500 Received: from posta.unizar.es (posta.unizar.es [155.210.11.16]) by relay.unizar.es (8.11.1/8.11.1) with ESMTP id f1198un07128 for ; Thu, 1 Feb 2001 10:08:56 +0100 (MET) Received: from qo_ttf-p3 ([155.210.88.182]) by posta.unizar.es (8.9.1/8.9.1) with SMTP id KAA29198 for ; Thu, 1 Feb 2001 10:07:41 +0100 (MET) Message-ID: <002f01c08c2e$a641faa0$b658d29b@qo_ttf-p3> From: "Jesus Orduna" To: Subject: DFT hyperpolarizabilities in G98 Date: Thu, 1 Feb 2001 10:09:14 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002C_01C08C37.07DB8210" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3612.1700 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 This is a multi-part message in MIME format. ------=_NextPart_000_002C_01C08C37.07DB8210 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I am interested in the calculation of DFT first hyperpolarizabilities = (beta). To the best of my knowledge, G98 is not able to calculate = analytical hyperpolarizabilities by dft methods (even though the manual = is rather confussing concerning this point). The only way I have been = able to calculate beta is using the keyword POLAR=3DEnOnly, that causes = the calculation of beta as the second numerical derivative of the dipole = moment with respect to the electric field. Since analytical = polarizabilities (alfa) are available in G98 I wonder if there is a way = to calculate beta as the first numerical derivative of alfa which should = lead to a more rapid and precise calculation. A second question concerns the calculation of second = hyperpolarizabilities (gamma). Can they be calculated in G98 using = either HF or DFT methods. Regards =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Jesus Orduna Instituto de Ciencia de Materiales de Aragon Unidad de Nuevos Materiales Org=E1nicos Facultad de Ciencias CSIC-Universidad de Zaragoza E-50009 Zaragoza (Spain) Phone/FAX: +34 976 761194 e-mail: jorduna@posta.unizar.es =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ------=_NextPart_000_002C_01C08C37.07DB8210 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
I am interested in the calculation of DFT first=20 hyperpolarizabilities (beta). To the best of my knowledge, G98 is not = able to=20 calculate analytical hyperpolarizabilities by dft methods (even though = the=20 manual is rather confussing concerning this point). The only way I have = been=20 able to calculate beta is using the keyword POLAR=3DEnOnly, that causes = the=20 calculation of beta as the second numerical derivative of the dipole = moment with=20 respect to the electric field. Since analytical polarizabilities (alfa) = are=20 available in G98 I wonder if there is a way to calculate beta as the = first=20 numerical derivative of alfa which should lead to a more rapid and = precise=20 calculation.
 
A second question concerns the calculation of second = hyperpolarizabilities (gamma). Can they be calculated in G98 using = either =20 HF or DFT methods.
 
Regards
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Jes= us=20 Orduna
Instituto de Ciencia de Materiales de Aragon
Unidad de = Nuevos=20 Materiales Org=E1nicos
Facultad de Ciencias
CSIC-Universidad de=20 Zaragoza
E-50009 Zaragoza (Spain)
Phone/FAX: +34 976 = 761194
e-mail: jorduna@posta.unizar.es
=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
------=_NextPart_000_002C_01C08C37.07DB8210-- From chemistry-request@server.ccl.net Thu Feb 1 05:33:28 2001 Received: from mserv3.dl.ac.uk (IDENT:root@mserv3.dl.ac.uk [148.79.80.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11AXSw13315 for ; Thu, 1 Feb 2001 05:33:28 -0500 Received: from tca7.dl.ac.uk (tca7.dl.ac.uk [193.62.112.105]) by mserv3.dl.ac.uk (8.9.3/8.9.3/[ref postmaster@dl.ac.uk]) with ESMTP id KAA25163; Thu, 1 Feb 2001 10:32:18 GMT Received: from dl.ac.uk by tca7.dl.ac.uk (8.9.3/1.1.27.5/13Jul00-0147PM) id KAA0000228628; Thu, 1 Feb 2001 10:26:52 GMT Message-Id: <200102011026.KAA0000228628@tca7.dl.ac.uk> Sender: H.G.Schreckenbach@dl.ac.uk Date: Thu, 01 Feb 2001 10:26:46 +0000 From: Georg Schreckenbach <"h.g.schreckenbach"@dl.ac.uk (Georg Schreckenbach)> Reply-To: Georg Schreckenbach Organization: CLRC Daresbury Lab X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V5.0 alpha) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net CC: Ulrike Salzner Subject: programming language for chemistry students References: <20010131180109.B541@geneseo.ks.uiuc.edu> Content-Type: multipart/alternative; boundary="------------E4FBA3E7F530D5C7A49CE6F5" --------------E4FBA3E7F530D5C7A49CE6F5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everybody, this is a very interesting thread, and I cannot resist adding my $0.02 to it ... What I am mostly missing from the discussion so far is the question: WHY do you want to teach the students a programming language? What is this intended to achieve? Do you want them to be able to do computational chemistry? - Then the answer would probably be FORTRAN. Many arguments have been brought forward for this pojnt of view. Do you want them to gain skills that are useful in the job market, not necessarily working as a chemist? - By todays standards, the answer wold probably be C/C++ in this case. Do you want them to gain skills that they can apply right away? - Then perhaps JAVA isn't that bad, because they can use it for their websites etc., as has been pointed out. Do you want them to learn logical thinking? - Again, the answer would be different: this point of view has been discussed already, and I will not repeat it. I guess my point is that there is not just one 'right answer' to the question! Best regards, Georg -- Dr. Georg Schreckenbach phone: +44-1925-603849 CLRC Daresbury Laboratory FAX: +44-1925-603634 Daresbury, Warrington, Cheshire, WA4 4AD, UK h.g.schreckenbach@dl.ac.uk http://www.geocities.com/gschreckenbach/ --------------E4FBA3E7F530D5C7A49CE6F5 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everybody,

this is a very interesting thread, and I cannot resist adding my $0.02 to it ...

What I am mostly missing from the discussion so far is the question: WHY do you want to teach
the students a programming language? What is this intended to achieve?

Do you want them to be able to do computational chemistry? - Then the answer would probably
be FORTRAN. Many arguments have been brought forward for this pojnt of view.

Do you want them to gain skills that are useful in the job market, not necessarily working as a
chemist? - By todays standards, the answer wold probably be C/C++ in this case.

Do you want them to gain skills that they can apply right away? - Then perhaps JAVA isn't that bad,
because they can use it for their websites etc., as has been pointed out.

Do you want them to learn logical thinking? - Again, the answer would be different: this point
of view has been discussed already, and I will not repeat it.

I guess my point is that there is not just one 'right answer' to the question!

Best regards, Georg
  

--
Dr. Georg Schreckenbach          phone: +44-1925-603849
CLRC Daresbury Laboratory      FAX: +44-1925-603634
Daresbury, Warrington, Cheshire, WA4 4AD, UK
h.g.schreckenbach@dl.ac.uk   http://www.geocities.com/gschreckenbach/
  --------------E4FBA3E7F530D5C7A49CE6F5-- From chemistry-request@server.ccl.net Thu Feb 1 05:06:24 2001 Received: from gatekeeper.bnfl.co.uk ([193.35.7.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11A6Mw13064 for ; Thu, 1 Feb 2001 05:06:22 -0500 Received: by gatekeeper.bnfl.co.uk; id KAA08845; Thu, 1 Feb 2001 10:05:01 GMT From: Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper.bnfl.co.uk via smap (3.2) id xma008802; Thu, 1 Feb 01 10:04:54 GMT Received: from ASN027.bnfl.com (unverified) by ant008.spr.bnfl.com (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Thu, 1 Feb 2001 10:00:12 +0000 Received: from BNotesMTA1.sell.bnfl.com ([10.30.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id KAA08539 for ; Thu, 1 Feb 2001 10:02:55 GMT Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.7 (934.1 12-30-1999)) id 002569E6.00376C8B ; Thu, 1 Feb 2001 10:05:22 +0000 X-Lotus-FromDomain: BNFL To: CHEMISTRY@ccl.net Message-ID: <002569E6.00376C33.00@BNotesMTA1.sell.bnfl.com> Date: Thu, 1 Feb 2001 10:05:28 +0000 Subject: Re: CCL:programming language Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline As an addendum, a colleague also suggested as a tool which will have greater use in terms of employability is SQL. Generally we all agreed though that the most important principle is to teach people HOW to program - the actual language is less important. Scott Owens "Dr. Richard Wood" on 31/01/2001 15:12:51 To: chemistry@ccl.net cc: (bcc: Scott L Owens/R&T/Risley/BNFL) Subject: CCL:programming language Ulrike Salzner wrote: > We are a chemistry department and our first year students take a computer > science cours learning JAVA. They told me that they don't think it is of > any use to them. > > I would like to collect opinions which programming language is most useful > for chemists. Let's assume they are learning only one. From chemistry-request@server.ccl.net Thu Feb 1 04:03:31 2001 Received: from funnel.chemeng.ed.ac.uk (funnel.chemeng.ed.ac.uk [129.215.122.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1193Uw12487 for ; Thu, 1 Feb 2001 04:03:30 -0500 Received: from eng.ed.ac.uk ([129.215.122.157]) by funnel.chemeng.ed.ac.uk (8.9.3/8.9.3) with ESMTP id JAA27461 for ; Thu, 1 Feb 2001 09:03:25 GMT Message-ID: <3A7926DA.507ACD00@eng.ed.ac.uk> Date: Thu, 01 Feb 2001 09:05:30 +0000 From: "Dr Mark J. Biggs" Organization: The University of Edinburgh X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Programming language References: <3.0.5.32.20010131130558.0087eda0@semovm.semo.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit There is often too much emphasis placed on "the language". Which language is taught is much less relevent than the need for them to learn about programming concepts (all the way from recursive execution through to OO through to debugging/quality concepts) and how to tack problems in a logical way. If you get those two things right, the average student should have no problems picking up any language. "Anthony J. Duben" wrote: > I hope that this discussion does not become a religiouswar, but I believe that any modern language would be > quite suitable -- C, FORTRAN, C++, JAVA -- are all good > candidates. You are not training chemists to maintain > legacy code (much of which is in FORTRAN, plenty is in C, > and some more in C++). You want the students to learn > how to think algorithmically. JAVA is a good candidate > because of its object-orientation is more thoroughly > part of it than C++. By the time the students graduate > and maybe finish grad school, whatever language they learn > now will have gone through another 3 editions. > > So, I would urge the students to get on with it and > really work hard at it. The hardest computer language > to learn is the first one in which they need to learn > how to think in algorithms. The next one to learn is > a lot easier. > > Anthony J. Duben (ajduben@semovm.semo.edu) > > ******************************************************** > Anthony J. Duben > Professor and Chairman > Computer Science Dept., MS 5950 > Southeast Missouri State University > 1 University Plaza > Cape Girardeau MO 63701-4799 > phone: 573-651-2194 > fax: 573-651-2791 > e-mail: ajduben@semovm.semo.edu > or c867buc@semovm.semo.edu > > "Education is not the filling of a pail > but the lighting of a fire." > -- William Butler Yeats > > "Amateurs talk strategy; > professionals talk logistics." > -- Gen. Omar N. Bradley > > > -= 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 From chemistry-request@server.ccl.net Thu Feb 1 07:37:41 2001 Received: from spider.irb.hr (spider.irb.hr [161.53.131.146]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11Cbdw14939 for ; Thu, 1 Feb 2001 07:37:40 -0500 Received: from localhost (boris@localhost) by spider.irb.hr (8.10.0/8.10.0) with ESMTP id f11IaXR21264 for ; Thu, 1 Feb 2001 13:36:33 -0500 Date: Thu, 1 Feb 2001 13:36:33 -0500 (EST) From: Borislav Kovacevic Subject: solvation energy on protonated molecule with N To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear cclers, I have problem with calculation of solvation energy on one protonated molecule possessing nitrogen atoms. I used gaussian 98 and b3lyp/6-311+g** level of theory. The job did not converge. This is the end of output: Iteration number 199 MaxDiff 0.279311485556E-05 Iteration number 200 MaxDiff 0.276338742653E-05 Maximum number of iterations exceeded. Error termination via Lnk1e in /usr/local/chemistry/g98/l117.exe. I tried to increase number of iteration, but without any success =========================================================================== Boris Kovacevic Phone: (385) (1) 4561-117 Quantum chemistry group Fax: (385) (1) 4561-118 Institut Rudjer Boskovic e-mail: boris@spider.irb.hr Bijenicka 54, 10000 Zagreb http: Croatia ============================================================================ From chemistry-request@server.ccl.net Thu Feb 1 09:53:37 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11Erbw15531 for ; Thu, 1 Feb 2001 09:53:37 -0500 Received: from cornell.edu (phobos.mbg.cornell.edu [128.84.203.151]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA05690; Thu, 1 Feb 2001 09:53:36 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3A797953.1A556D5C@cornell.edu> Date: Thu, 01 Feb 2001 09:57:23 -0500 From: Richard Gillilan Reply-To: reg8@cornell.edu X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-3 i686) X-Accept-Language: en MIME-Version: 1.0 To: Irene Newhouse CC: chemistry@ccl.net Subject: Re: CCL:programming language References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In a C++ vs Fortran performance summary I wrote for this list a couple years ago, (see http://www.ccl.net/cgi-bin/ccl/message.cgi?1999+10+26+007 ) I cited a paper that gives some examples where C++ is actually faster than FORTRAN. It appears that the paper is no longer available online, but I'm fairly certain I have an electronic copy archived somewhere: The best paper I've seen so far was suggested by Oliver Kohlbacher: "Will C++ be faster than Fortran?" by Veldhizen and Jernigan (downloadable at www.acl.lanl.gov/iscope97/agenda.htm) The authors give some real-world examples where C++ is as fast or faster than Fortran. They also list reasons why C++ has been slower in the past and give some features of the language that may allow it to be faster in the future. This reference is a bit outdated now, but I don't know of anything like it more recently. If you'd like a copy, I'll see if I can find the file. Though I've never stopped to tally up statistics on languages, in my 7 years at a national supercomputing center (CTC), I'd certainly agree that the vast majority of scientific code was FORTRAN. It's interesting to note, however, that two of the largest center-wide projects underway at the CTC now (genomics and digital materials) are being implemented in C++. These are very complex, very numerically intensive projects that are being implemented by folks who are well versed in compilers and code optimization and have done plenty of FORTRAN in the past. That's not to say I think Object-oriented programming is right for all jobs, or that FORTRAN is on it's way out, but that C++ and OOP work just fine for scientific computing. If I recall from a talk I heard 10yr ago or more, CAChe scientific was one of the early commercial comp chem software developers to go C++ (http://www.cachesoftware.com/), though I'm not sure to what extent. VMD/NAMD from Klaus Schulten's group is a excellent recent example of clean, well-written open code ... well worth emulating. One of the big values supposedly offered by OOP is much better ability to create, maintain and extend huge code bases. Anecdotally, I certainly feel this way, but it would be interesting to see if companies and groups are measurably doing better when they adopt this style. I suspect only time will tell .... truely extensible, maintainable code will live on when all its original authors are gone and continue to grow and evolve. Richard From chemistry-request@server.ccl.net Thu Feb 1 07:45:00 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11Cj0w14970 for ; Thu, 1 Feb 2001 07:45:00 -0500 Received: by XENA with Internet Mail Service (5.5.2650.21) id ; Thu, 1 Feb 2001 12:42:23 -0000 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9A0CBC70@GABRIELLE> From: "Robinson, James" To: "'Joe M Leonard'" , "'CCL'" Subject: RE: programming language Date: Thu, 1 Feb 2001 12:42:18 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" These students will need jobs and you must give the skills they will need in an ever evolving workplace. How many companies use Fortran as opposed to C++/Java? The ability to program comes from the ability to think in the correct manner, not from learning a single language. Joe Leonard is right in declaring that programming skills are more important that language familiarity. James -----Original Message----- From: Joe M Leonard [mailto:jle@world.std.com] Sent: 01 February 2001 00:44 To: chemistry@ccl.net Subject: CCL:programming language Folks, I've tried to avoid emailing a reply to this, as it's basically a flame war with no real resolution - but I like wearing Nomex underwear... Learning Fortran alone is career-limiting, period. There are too many restrictions - no memory allocation, limited system calls, poor string handling, etc. "Good code" written in many languages will outperform "bad code" written in Fortran. Algebraic/formulaic code looks pretty much the same in any language... If one has to maintain dusty-deck codes, then yeah, Fortran is required. However, knowing a second language lets one do the CPU-intensive stuff in Fortran (if one desires) and the "interacts with world" stuff in a more-suited language. Select the tool for the task. Rather than concentrating on a language, concentrate on how programs are designed, constructed and maintained. A small bit of C lets one, for example, ship a single binary which is capable of sizing itself - rather than forcing a set of binaries for differing problem-size memory requirements. Finally, Fortran has never been loved by those who write compilers (except for some for-purchase versions). Therefore, if you're limiting yourself to Open Source tools, writing in Fortran will slow you down as nobody's taken the time to add the necessary optimizing stuff to g77. Times change - I've written miles of stuff in various languages, and (repeating myself, sorry) the trick is to write code which solves the problem and can be maintained. Don't teach "Fortran Programming", teach "Programming". If you want to teach numerically intensive programming, use whatever language you want, and avoid the language features which do not positively contribute to performance... Also consider the effect of debugging and testing tools - graduate student time is cheap, but it can be hard on the grad student. Joe jle@world.std.com -= 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 From chemistry-request@server.ccl.net Thu Feb 1 08:02:09 2001 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11D29w15049 for ; Thu, 1 Feb 2001 08:02:09 -0500 Received: from pat.biochem.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Thu, 1 Feb 2001 13:02:08 +0000 Received: from bsmir18 (bsmir18 [128.40.46.21]) by pat.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id MAA12088 for ; Thu, 1 Feb 2001 12:59:59 GMT Date: Thu, 1 Feb 2001 12:59:58 +0000 ("GMT) From: Irilenia Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: Concentrations of AMP and GMP (and languages!) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII My most sincere apologies for the off-topic question but I suspect that some of you may know the answer to the following question: What is the relative concentration of AMP and GMP in the cell? (and in general whether adenosine is more or less or equally likely to be floating around in a living cell). I don't expect numbers of course. Any hints on where to find the answer (if it is known!) would be appreciated. And since I'm here my humble opinion on the programming course. What I find is really important is to teach students good programming techniques. Languages will come and go and the students may or may not follow a career in computational chemistry. But if you can teach them to write readable and re-usable code, now that's a challenge! Irilenia ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk tel. 020 7679 2171 fax. 020 7679 7193 "Socrates and Marx and the other wise people are all dead...and I don't feel too well lately myself.." From chemistry-request@server.ccl.net Thu Feb 1 10:59:59 2001 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11Fxxw16270 for ; Thu, 1 Feb 2001 10:59:59 -0500 Received: from socrates-a.ucl.ac.uk by mail-c.bcc.ac.uk with SMTP (Mailer); Thu, 1 Feb 2001 15:59:01 +0000 From: uccatvm Message-Id: <26447.200102011559@socrates-a.ucl.ac.uk> Subject: OPLS potential for tryptophan To: chemistry@ccl.net (CCL) Date: Thu, 1 Feb 2001 15:59:54 +0000 (GMT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers, I am trying to get an OPLS potential for tryptophan. Jorgensen's paper on OPLS potential functions for proteins (W.L. Jorgensen, J. Tirado- Rives, J.Am.Chem.Soc. 110, 1657, 1988) contains OPLS parameters for tryptophan. According to the paper, standard geometries were used. However, I can't find standard values for all the tryptophan bond lengths and angles. Could someone give me a pointer where to find them? Secondly, as far as I am aware, there is no all-atom OPLS potential for tryptophan (the 1988 potential uses united atom CH groups). Is this correct? Best wishes, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)207-679-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@server.ccl.net Thu Feb 1 08:56:54 2001 Received: from lancelot.imb-jena.de (lancelot.imb-jena.de [192.124.248.76]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11Durw15291 for ; Thu, 1 Feb 2001 08:56:54 -0500 Received: (from pineda@localhost) by lancelot.imb-jena.de (SGI-8.9.3/8.8.8) id OAA33072; Thu, 1 Feb 2001 14:56:53 +0100 (CET) From: pineda@imb-jena.de (Felipe Pineda) Message-Id: <10102011456.ZM33108@lancelot.imb-jena.de> Date: Thu, 1 Feb 2001 14:56:53 +0000 In-Reply-To: David van der Spoel "Re: CCL:Cluster analysis" (Jan 17, 12:16pm) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@ccl.net Subject: Cluster analysis: summary Cc: doree.sitkoff@bms.com Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.110102011456.ZM33108.imb-jena.de" --PART-BOUNDARY=.110102011456.ZM33108.imb-jena.de Content-Description: Text Content-Type: text/plain ; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Zm-Decoding-Hint: mimencode -q -u Dear CCLers! here is a summary of the responses i got to my posting and some personal comments on a couple of them. -------------------------------------------------------------------------= ----- My original enquiry: i would be very grateful for any pointer to a software tool (utility in commercial or academic s/w, standalone tool) which is able to perform suc= h an analysis on a set of conformers typically sampled by some FF MD protocol (e.g.,simmulated annealing) and to build families of conformations displa= ying similarity to each other with respect to an user defined structural featu= re (backbone conformation, for example) to a given extent (some rmsd thresho= ld) specified by the user. i used some years ago an insightII macro called family.bcl written by Don Mackay, 1991, which do this with the help of an= external program called also family: (...) but in the meantime there are maybe new, more efficient tools out there. -------------------------------------------------------------------------= ----- The answers: 1. from David van der Spoel The gromacs MD package has a clustering tool: http://md.chem.rug.nl/~gmx 2. from Carlos Simmerling moil-view is a free program for SGI that does cluster analysis. there is a link to it from my page -> http://comp.chem.sunysb.edu/carlos my comment: we downloaded the unix distribution of moil-view v9.1 and used the progra= m for performing the cluster analysis. initially the only difficulty consisted = in getting our trajectories (available both in pdb and msi's sequential arc format) in the formats supported by moil-view, i.e., DCD/PATH/AMBER/AMBER= PBC). we tried to do this by reading the pdb traj. files with VMD v1.6 for wind= ows, but, for some unknown reason, the generated binary DCD files could not be= read by moil-view. although latter was able to read and cluster some trajector= ies in AMBER (crd) format also generated with VMD, other cdr files contained for= mat errors, so we had to do the corresponding conversion (pdb -> cdr) with a = small piece of fortran code. moil-view does the job fine and its functionality = is very similar to that of the old insight macro i mentioned above. 3. from S=E9rgio Emanuel Galembeck In my lab we use XCluster software to make cluster analysis after conformational search. Results are very good and agree with experimental information. This software is part of MacroModel suite. 4. from Peter Shenkin : MacroModel, from Schrodinger, Inc., includes XCluster, which is described in J. Comp. Chem., v15, #8, 899-916 (1994). See www.schrodinger.com for some more details (including the manual) 5. from Doree F Sitkoff I've used the program NMRCLUST, freely available at http://neon.chem.le.ac.uk/nmrclust/protocol.html 5. from Jodi Shaulsky 5.1. If you have InsightII the Analysis module allows you to create and manipulate cluster graphs from which families can be defined. This is done using the Trajectory/Construct_Graph with the 'Cluster_Graph' button 'on' 5.2. Did you look at the Family command under the Trajectory pulldown. It look= s like you can do everything that the script would do using command Family.= It will create an assembly of the comformers that meet the criteria you set. This assembly can then be writen out to a file. I looked around for the macro called family but was not able to locate it= =2E my comment: after generating the clustergraph (i.e. the rmsd matrix the clustering is= based on) i was playing around for a while with the Analysys/Trajectory/Family = pull down, as advised. unfortunately, i was not able to perform the cluster analysis, but only to generate a single family of conformers at each time= based on different criteria. i am convinced that it should be possible to write= a simple insight macro using the (new) family command, but that was not rea= lly the solution i was looking for. Thanks a lot to everybody who responded. Best regards felipe -- = ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * * web: www.imb-jena.de/~pineda * *"In the world predominates the suffering and prevails the injustice"* * G. Garcia Marquez, colombian writer, Lit. Nobel Prize laureat * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * = = * my personal opinion, not an official statement of my employer * = = ********************************************************************** --PART-BOUNDARY=.110102011456.ZM33108.imb-jena.de-- From chemistry-request@server.ccl.net Thu Feb 1 05:03:01 2001 Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11A30w13035 for ; Thu, 1 Feb 2001 05:03:01 -0500 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id KAA18835; Thu, 1 Feb 2001 10:03:05 GMT Message-ID: <3A793466.5467C981@nibsc.ac.uk> Date: Thu, 01 Feb 2001 10:03:18 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: Alessandro , chemistry@ccl.net Subject: Re: CCL:Modelling of DNA-Protein interaction References: <3A7822C2.EC86D603@csrsrc.mi.cnr.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Allesandro Check out the references below: Several programs are available for docking two macromolecules when one of them (typically the protein) is held rigid and then replaced by a grid. The Sterberg group have a code (Multidock) which allows full flexibility, see their web page http://www.bmm.icnet.uk/multidock/multidock.html The Nussinov group (ref 4) are also publishing reports on flexible docking but I am not sure if their codes are available. Their work focusses on protein-protein complexes. (1) Predictive docking of protein-protein and protein-DNA complexes. Sternberg MJ, Gabb HA, Jackson RM Curr Opin Struct Biol. 1998 Apr;8(2):250-6. Review. (2) Modelling repressor proteins docking to DNA. Aloy P, Moont G, Gabb HA, Querol E, Aviles FX, Sternberg MJ Proteins. 1998 Dec 1;33(4):535-49. (3) Monte Carlo docking of protein-DNA complexes: incorporation of DNA flexibility and experimental data. Knegtel RM, Boelens R, Kaptein R Protein Eng. 1994 Jun;7(6):761-7. (4) A method for biomolecular structural recognition and docking allowing conformational flexibility. Sandak B, Nussinov R, Wolfson HJ J Comput Biol. 1998 Winter;5(4):631-54. Hope this helps. Mark Alessandro wrote: > Dear cclers, > > I am looking for some good reviews about DNA-Protein interaction, both > on modelling and calculations. > Despite some experiences on protein studies, I have no idea on DNA > problems... so pratical suggestion on this topics are gratefully > accepted, too. > > This is a "first look" search, just for getting an idea of the state of > the art, so every good information could be useful. > > Thanks a lot. > > Ale > > -= 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 -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Thu Feb 1 04:59:19 2001 Received: from gatekeeper.bnfl.co.uk ([193.35.7.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f119xIw12989 for ; Thu, 1 Feb 2001 04:59:18 -0500 Received: by gatekeeper.bnfl.co.uk; id JAA07425; Thu, 1 Feb 2001 09:57:57 GMT From: Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper.bnfl.co.uk via smap (3.2) id xma007362; Thu, 1 Feb 01 09:57:46 GMT Received: from ASN027.bnfl.com (unverified) by ant008.spr.bnfl.com (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Thu, 1 Feb 2001 09:53:07 +0000 Received: from BNotesMTA1.sell.bnfl.com ([10.30.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id JAA07882 for ; Thu, 1 Feb 2001 09:55:50 GMT Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.7 (934.1 12-30-1999)) id 002569E6.0036C5BA ; Thu, 1 Feb 2001 09:58:15 +0000 X-Lotus-FromDomain: BNFL To: CHEMISTRY@ccl.net Message-ID: <002569E6.0036C3A7.00@BNotesMTA1.sell.bnfl.com> Date: Thu, 1 Feb 2001 09:58:17 +0000 Subject: Re: CCL:programming language Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Hi there, probably offering an unusual standpoint here and I know that this message weill probably cause the usual c vs fortran arguments, but from and industrial perspective and in terms of producing students that will have the most appropriate programming skills no matter what area they move into (most students do NOT go on to do programming based research). My offer on this would be Visual Basic. Most people I asked in our group have used visual basic and spreadsheet macros, whereas only 3 out of 17 have used C (or a variant) and only 2 have used Fortran. So you want to produce students with the correct skills they will need to use, data manipulation is more important to all students than either C or fortran programming. Just my humble opinion (which I am sure will be completely ignored by most academic depts as Visual Basic is proprietory and not trendy enough). Scott Owens "Dr. Richard Wood" on 31/01/2001 15:12:51 To: chemistry@ccl.net cc: (bcc: Scott L Owens/R&T/Risley/BNFL) Subject: CCL:programming language Ulrike Salzner wrote: > We are a chemistry department and our first year students take a computer > science cours learning JAVA. They told me that they don't think it is of > any use to them. > > I would like to collect opinions which programming language is most useful > for chemists. Let's assume they are learning only one. From chemistry-request@server.ccl.net Thu Feb 1 11:03:28 2001 Received: from mf104.infoweb.ne.jp (mf104.infoweb.ne.jp [210.131.99.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11G3Sw16294 for ; Thu, 1 Feb 2001 11:03:28 -0500 Received: from [192.168.1.55] by mf104.infoweb.ne.jp (8.9.3+3.2W/3.7W-10/13/99) with ESMTP id BAA15704 for ; Fri, 2 Feb 2001 01:03:21 +0900 Mime-Version: 1.0 X-Mailer: Macintosh Eudora Version 4.3.2-J Message-Id: Date: Fri, 2 Feb 2001 01:02:07 +0900 To: chemistry@ccl.net From: Narushi Goto Subject: G98 on LinuxPPC Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hi all, Has anyone successfully compiled g98 on LinuxPPC using g77 or Absoft Pro FORTRAN? If someone knows the compile options and/or tips, please advice me. Regards, Narushi From chemistry-request@server.ccl.net Thu Feb 1 13:25:21 2001 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11IPKw17697 for ; Thu, 1 Feb 2001 13:25:20 -0500 Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay2.scripps.edu (8.11.0/TSRI-4.0r) with ESMTP id f11INKa25975; Thu, 1 Feb 2001 10:23:20 -0800 (PST) Received: (from case@localhost) by gamow.scripps.edu (8.9.1a/TSRI-2.8) id KAA215038; Thu, 1 Feb 2001 10:23:19 -0800 (PST) Date: Thu, 1 Feb 2001 10:23:19 -0800 From: David Case To: Avijit Ghosh Cc: CHEMISTRY@ccl.net Subject: Re: CCL:GPL'd MD packages Message-ID: <20010201102319.F214706@gamow.scripps.edu> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: ; from avijit@cs.cornell.edu on Wed, Jan 31, 2001 at 06:42:02PM -0500 On Wed, Jan 31, 2001, Avijit Ghosh wrote: > > I was wondering whether anyone has any GPL'd code for MD? > Particularly, whether there are any GPL'd force field > implementations out there (I.E. MM*/OPLS*/AMBER* ). NAB (Nucleic acid builder) implements the Amber95 force field. It includes generalized Born calculations, but *not* periodic boundary conditions simulations, so it may or may not satisfy particular needs. In spite of the name, it is designed to work on proteins as well as nucleic acids. Whether or not the code itself (mainly in file sff.c) would be useful to transfer to other applications is of course a subjective decision, but you are certainly free to do anything allowed by the terms of GPL. See my web page (below) for more info. ....good luck...dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== From chemistry-request@server.ccl.net Thu Feb 1 13:47:09 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11Il8w17868 for ; Thu, 1 Feb 2001 13:47:08 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA04362 for ; Thu, 1 Feb 2001 13:47:08 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A79ADC0.B11A128E@cornell.edu> Date: Thu, 01 Feb 2001 13:41:04 -0500 From: "Dr. Richard Wood" Organization: Cornell University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:programming language/Regarding Douglas Smith's comments References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr. Smith- Two comments: First of all, she stated that the students didn't think Java was useful to them. So shouldn't Java be out of the mix of our disscussions? Secondly, I wonder why a lot of MD codes are/were written in Fortran and not C++? When i was a Ph. D. student, there was an attempt in our group to convert our Fortran based MD program into a C++ based one. However, it soon hit us that there were things that one could not do with C++ that one could do with the Fortran code. Bear in mind, this was less than 2 years ago. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Feb 1 16:26:00 2001 Received: from rock.helsinki.fi (rock.helsinki.fi [128.214.3.50]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11LPxw19053 for ; Thu, 1 Feb 2001 16:25:59 -0500 Received: from localhost (sundius@localhost) by rock.helsinki.fi (8.9.3/8.9.3) with ESMTP id XAA29957 for ; Thu, 1 Feb 2001 23:25:59 +0200 (EET) Date: Thu, 1 Feb 2001 23:25:59 +0200 (EET) From: Tom Sundius X-Sender: To: Subject: Re: CCL:programming language In-Reply-To: <5FD8C12EECBBD4119DD10002B3027B9A0CBC70@GABRIELLE> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII So now we have also got this language debate here in CCL. I have the same opinion as James. It is not so important what computer language is being taught in introductory programming courses for science students. It is more important that some simple principles of programming are taught, and for that purpose you can use Fortran, C, C++, Java,... I have taught introductory programming courses for Physics students for many years now. In the beginning I used Pascal, but later on I switched over to Fortran (lately Fortran 90). One of my colleagues gives a similar course based on C. Object-oriented stuff etc. can be saved for more advanced courses. In the beginning it is most important to get some familiarity with principles. We usually start with MATLAB, which is easier, since programs written in MATLAB can be immediately checked. After that we proceed to simple programming. On Thu, 1 Feb 2001, Robinson, James wrote: > These students will need jobs and you must give the skills they will need in > an ever evolving workplace. How many companies use Fortran as opposed to > C++/Java? The ability to program comes from the ability to think in the > correct manner, not from learning a single language. Joe Leonard is right in > declaring that programming skills are more important that language > familiarity. > > James .... Greetings, Tom Tom Sundius University of Helsinki, Department of Physics phone +358-9-191 8339 P.O.Box 9, FIN-00014 Helsinki, Finland fax +358-9-191 8680 From chemistry-request@server.ccl.net Thu Feb 1 16:21:23 2001 Received: from be-research.ucsd.edu (be-research.ucsd.edu [132.239.236.13]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11LLMw19024 for ; Thu, 1 Feb 2001 16:21:23 -0500 Received: from localhost (dsteiger@localhost) by be-research.ucsd.edu (8.11.1/8.11.1) with ESMTP id f11LL3m03800; Thu, 1 Feb 2001 13:21:07 -0800 (PST) Date: Thu, 1 Feb 2001 13:21:02 -0800 From: Don Steiger To: Jim Phillips cc: "Mark A. Zottola" , Ulrike Salzner , chemistry@ccl.net Subject: Re: CCL:programming language In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 31 Jan 2001, Jim Phillips wrote: > Hi, > > I would say FORTRAN is the default scientific programming language because > plain vanilla FORTRAN compiles just about everywhere. Of course, with a > language like Java it will run the same everywhere as well whereas FORTRAN > leaves behaviors like aliasing undefined. FORTRAN also teaches bad > programming practices like fixed size arrays, global data, and all caps. > This may be true about FORTRAN77 but it is definitely not true about FORTRAN90/95. The handling of global data and the dynamic manipulation of array size is at least as good in FORTRAN90/95 as it is in C/C++. The only reason not to use FORTRAN90/95 in large numerical simulations is that it will soon become extinct because nobody is using it. From chemistry-request@server.ccl.net Thu Feb 1 18:20:31 2001 Received: from smtpsrv1.isis.unc.edu (smtpsrv1.isis.unc.edu [152.2.1.138]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f11NKVw19728 for ; Thu, 1 Feb 2001 18:20:31 -0500 Received: from bock.chem.unc.edu.unc.edu (bock.chem.unc.edu [152.2.48.182]) by smtpsrv1.isis.unc.edu (8.9.3/8.9.1) with ESMTP id SAA00309; Thu, 1 Feb 2001 18:20:31 -0500 (EST) Sender: jochen@bock.chem.unc.edu To: "Dr. Richard Wood" Cc: chemistry@ccl.net Subject: Re: CCL:programming language/Regarding Douglas Smith's comments References: <3A79ADC0.B11A128E@cornell.edu> User-Agent: XEmacs/Gnus X-Attribution: yogi X-Face: -%Z4EZ6iY'4m:wiK:!v Organization: University of North Carolina Date: 01 Feb 2001 18:20:32 -0500 Message-ID: <86k87axa67.fsf@bock.chem.unc.edu> Lines: 19 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii >>>>> Richard Wood wrote on Thu, 01 Feb 2001 13:41:04 -0500: Richard> When i was a Ph. D. student, there was an attempt in our Richard> group to convert our Fortran based MD program into a C++ Richard> based one. However, it soon hit us that there were things Richard> that one could not do with C++ that one could do with the Richard> Fortran code. I think with this statement you should tell us what can be in Fortran and not in C++? Or probably you need to clarify tour statement a bit further. Greetings, Jochen -- University of North Carolina phone: 919-962-1579 Department of Chemistry fax: 919-843-6041 Venable Hall CB#3290 Chapel Hill, NC 26599, USA From chemistry-request@server.ccl.net Thu Feb 1 20:36:05 2001 Received: from mailhost.cle.ameritech.net (mpdr0.cleveland.oh.ameritech.net [206.141.223.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f121a5w20989 for ; Thu, 1 Feb 2001 20:36:05 -0500 Received: from ballg.popmail.csuohio.edu ([64.109.43.235]) by mailhost.cle.ameritech.net (InterMail v4.01.01.07 201-229-111-110) with ESMTP id <20010202013404.MWMZ923.mailhost.cle.ameritech.net@ballg.popmail.csuohio.edu> for ; Thu, 1 Feb 2001 20:34:04 -0500 Message-Id: <5.0.2.1.0.20010201202941.009eee60@popmail.csuohio.edu> X-Sender: d.ball@popmail.csuohio.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Thu, 01 Feb 2001 20:32:08 -0500 To: chemistry@ccl.net From: "David W. Ball" Subject: large G2 job Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed I have been trying to perform G2 calculations on a rather large system, C10H16 -- unsuccessfully. I don't know if it's memory or processor or file size issues, but no matter. It does beg the question, though: what's the largest system (ITO atomic centers or # of electrons) that G2 or G3 has been successfully applied to? Warning to respondents: you may be queried on how you did it! Best, David