From owner-chemistry@ccl.net Tue May 10 07:56:01 2011 From: "Konrad Hinsen hinsen-#-cnrs-orleans.fr" To: CCL Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN? Message-Id: <-44609-110510034328-26253-p8T8UUgnivA9g3SUQ2rfsQ]_[server.ccl.net> X-Original-From: Konrad Hinsen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Date: Tue, 10 May 2011 09:43:08 +0200 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Konrad Hinsen [hinsen_+_cnrs-orleans.fr] On 9 May 2011, at 13:00, Vincent Leroux vincent.leroux---loria.fr wrote: > I agree that Fortran, while it is not dead yet, is unfortunately > declining constantly, as most master students were never introduced > to it during their studies. Why is that so? I suspect that Fortran is in decline because it is a niche language: it was never used significantly outside of scientific computing. In the not-too-distant past, scientific computing was one of the driving forces in the development of computers and of software, so Fortran was important for computing in general. Nowadays, other computing applications have grown so much that scientific applications are no longer significant for the field as a whole. 30 years ago, finding new optimization techniques for Fortran was a hot topic in computer science, today nobody cares. With the exception of High-Performance Computing, whose survival is ensured by the money invested in there and the high visibility that attracts politicians at all levels, scientists will continue to adapt to a computing environment not made specifically for them. 20 years ago, I used a workstation designed for science and engineering, today I use a Mac, designed for multimedia and office applications. Software development goes the same way: most effort is invested in languages of interest for big application domains such as Web programming, scientists can best profit from that work by using those languages and tools and adding libraries for their own specific needs. A good illustration is Python, which is developed mostly for non-scientific areas, but which has attracted a significant scientific computing community centered around the NumPy library. > As for *teaching* scientific programming, I am a strong advocate of > Fortran 77, for several reasons: > > - The official F77 specifications are very concise, less than 100 > pages. Students can actually read them, and have a complete grasp > over the language. Is that possible with C, C++, Java, Python? Python is still a very simple language, although it has been (unfortunately, in my opinion) accumulating cruft recently. What's big is the libraries you need to learn to do anything non-trivial, but that's the same in any language. Java has its complex aspects, in particular concerning concurrency, but then other languages simply don't address that aspect and leave concurrent behaviour undefined. I'd say that Java is actually simpler than Fortran. Not that I am a Java fan (on the contrary), but that's for different reasons. C is reasonably complex, not very far from Fortran but different. C++ is probably the biggest mess ever invented in programming languages. > - What is "missing" in Fortran 77 (mostly direct memory access, > recursivity, definition of complex data structures) are indeed basic > features of any modern programming language, but those features > should never be "overused". I think it is good that students first > understand how it is possible to live without those in many cases, > so that they do not grow bad habits like systematically using more > pointers and OOP concepts than necessary... I strongly disagree. The highest priority in programming is correctness and clarity (way before performance). That requires expressive languages (-> data structures) and abstraction of low-level necessities (-> memory management). It's once you are a good programmer using good tools that you can afford to abandon high-level features when necessary for performance. > - This is not very important, but I have to mention that. No student > understands why the hell indexes should start at zero. I explain the reasons for this in my Python courses early on (when I introduce indexing) and insist on practicing this during the first two sessions. Hardly any student ever has problems with that afterwards. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research at khinsen dot fastmail dot net --------------------------------------------------------------------- From owner-chemistry@ccl.net Tue May 10 08:31:00 2011 From: "Andreas Bender, PhD ab454-#-cam.ac.uk" To: CCL Subject: CCL: "Connecting Structure to Function", Honouring Andy Vinter; Cambridge, 19-21 September 2011 Message-Id: <-44610-110510065506-4951-oRkMn8b9blMgjp6ct8/IJQ a server.ccl.net> X-Original-From: "Andreas Bender, PhD" Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 10 May 2011 11:54:19 +0100 Mime-Version: 1.0 Sent to CCL by: "Andreas Bender, PhD" [ab454###cam.ac.uk] Dear CCL'lers, Dear Cambridge Cheminformatics Friends, We would like to cordially invite you to a MGMS meeting in Cambridge (UK) on the topic of "Connecting Structure to Function: From Calculation to Experiment and Back Again" [ http://www.mgms.org/JGV_meeting/index.html ], an event organized to recognize and honour Andy Vinter and his contributions to the fields of computer-aided drug design and, more generally, intermolecular interactions and their driving forces. Andy will be well-known to many of you, from his times in pharmaceutical industry at Smith, Kline & French, from his years at the Chemistry Department of the University of Cambridge, as well as most recently, when deriving - and successfully establishing - directional force fields at his own independent computational drug discovery company, Cresset. It is this decades-long career and Andy's contributions to the field that we are paying tribute to. The meeting will take place from 19-21 September 2011, at Downing College, Cambridge. For further details and registration please visit the conference website at the following address: http://www.mgms.org/JGV_meeting/index.html To extend the announcement, we are also very happy to add that three student bursaries are available to attend the event, covering registration, accommodation and travel, which have been generously sponsored by Lhasa. For further information and details on how to apply please visit the following website: https://www.lhasalimited.org/news/item/lhasa_limited_student_bursary_2011/. Best wishes and we are looking forward to hopefully welcoming you to Cambridge in September! Cheers, Andreas -- Andreas Bender, PhD Lecturer for Molecular Informatics Unilever Centre, Cambridge University http://www-ucc.ch.cam.ac.uk Personal: http://www.andreasbender.de From owner-chemistry@ccl.net Tue May 10 10:28:00 2011 From: "Andreas Klamt klamt|-|cosmologic.de" To: CCL Subject: CCL: micelle structure (PDB) files Message-Id: <-44611-110510094022-16418-JAbZIIyVutLQVf99X7fk9A=server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 10 May 2011 15:40:11 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt^^^cosmologic.de] Dear CCLers, this time I like to post a question instead of commenting on other peoples questions: Does anyone know a larger reservoir of micelle structure data (most like stored in PDB format)? We would be interested in collecting such structures, either based on experimental data or on MD simulations. Maybe we could host a library of such files or a library of links to such files on our web site. In the moment we are especially interested in SLES micelles. Thanks in advance Andreas Klamt From owner-chemistry@ccl.net Tue May 10 16:40:01 2011 From: "Guntram Schmidt guntram.schmidt]=[chemie.uni-halle.de" To: CCL Subject: CCL:G: van-der-Waals-complex vs. weak forces Message-Id: <-44612-110510154504-11340-CPs6KNOvXEDWisFN5m7rVA|,|server.ccl.net> X-Original-From: "Guntram Schmidt" Date: Tue, 10 May 2011 15:45:00 -0400 Sent to CCL by: "Guntram Schmidt" [guntram.schmidt(-)chemie.uni-halle.de] Hello together! I want to exam some (mainly organic) crystal structures, which seem to be mainly held together by weak forces like Phenyl-H---O hydrogen bonds, Phenly-H---Phenyl hydrogen bonds or Pi-Pi-stacking. I cut out the corresponding dimers of the crystal structure and subjected them to geometry optimisation, using gaussian 09 with the input line #T opt freq b97d/6-31g(d,p)/auto=all which works quite well, resulting in minima for expected bonding, but striding away molecules for dimers which are not supposed to interact in a "bonding" way. Now having some optimized structures, is there anything to do to prove the nature of the "bonding"? How can I distinguish the "van-der-Waals complex" from a dispersion interaction or some kind of hydrogen bonding? Thanks a lot for suggestions on how to treat this problem, Guntram