Thursday, December 22, 2011

14th ICQC Registration Open

We are pleased to announce that the registration site is now open for
the 14th International Congress of Quantum Chemistry, to be held in
Boulder, Colorado, on June 25 - 30, 2012.

You can find the registration link on our web page:

Early-bird registration prices are available through the end of
February, 2012. We look forward to welcoming you to Boulder.


Josef Michl, chairman
Mark Gordon
Ken Houk
Keiji Morokuma

Mini-School on "Advanced Simulation Methods for Bio-molecular Systems", Nordita, Stockholm

We will be holding a 5-day Mini-School on "Advanced Simulation Methods
for Biomolecular Systems" at NORDITA, Stockholm, on Feb 27 -- March 2,

The focus of the school will be current state-of-the-art methods in
biomolecular simulation, including Molecular Dynamics, advanced Monte
Carlo techniques, all-atom force fields for biomolecules, coarse-graining
and multi-scale modeling.

The school is part of a longer Nordita scientific program on "Dynamics
of Biomolecular Processes". Many of the invited speakers will
contribute to the school, making it a great opportunity for PhD students
and post docs to learn about advanced computational techniques from
leading international researchers.

For more info and a link to the application form, see the school's

Accommodation during the mini-school will be provided by NORDITA
for all accepted students. The deadline for applications is Jan 10,

With best regards,

The organizers

Stefan Wallin (Lund University),
Ralf Eichhorn (Nordita),
Hans Behringer (University of Mainz),

Happy holidays!

Happy holidays from everyone at Proteins and wavefunctions!

Here is a picture from what I think we can safely assume was Caspers Steinmanns recent talk at JAXA (The Japanese Space Agency) about the effective fragment molecular orbital method, a linear scaling QM method implemented in GAMESS.

Saturday, December 10, 2011

Bond lengths, Avogadro, Google Docs, and gamification

Recently a colleague of mine, Henrik, lamented that at a recent oral exam many first year students had no clue what a typical bond length in a molecule is.  I am not a big fan of memorizing something that can be easily Googled, but we're talking order of magnitude here, not the last decimal place.

Read the rest of the entry over at Molecular Modeling Basics

Saturday, December 3, 2011

Code snippets on blogs

I had a brief discussion with Casper Steinmann about how to present code snippets in blog-posts. We both agreed that nice formatting is really important. We also agreed that our previous attempts to do so were (and still are) crummy.

One of the (easy) ways to set up nice formatting can be found over at CraftyFella:

Just put some stuff in your blogger template and all you have to do is wrap your code examples in HTML <pre>  tags. "Pre tags" denote a pre-defined format, and are often used to wrap around code examples, with the color coding pertaining to that particular code-language and an equispaced font, which makes it possible to use indentations properly.

Most popular programming languages are supported in this method. C, C++ C#, python, and probably many others. Hoever, no support for FORTRAN - quantum chemists beware. If you know of a user-friendly syntax highlighter that does FORTRAN, do leave a comment! Everybody loves FORTRAN.

Here is a simple example of how a dumb python script looks after using CraftyFella's guide to set things up:


def print_string(string):
    print string

hello_world = "Hello world, look at my fancy code formatting!"

for i in range(10):

... and a little bit of C++:

//! Return size of collection
//! \return size of collection
unsigned int size() const {
     return data_vector.size();

Thursday, December 1, 2011

WIREs Comput Mol Sci

Once in a while a new journal appears which have a fair opportunity of evolving into a high-impact journal come sufficient time. The Journal of Chemical Theory and Computation (JCTC) of William Jorgensen (Yale University) and Gustavo Scuseria (Rice University) is becomming one of these types of journals as of 2011/2012 and now a new journal has entered the field, namely the WILEY Interdisciplinary Reviews - Computational Molecular Science (WIREs Comput Mol Sci). The journal has as editor in chief the renowned Peter R. Schreiner (Justus-Liebig University Giessen) and what is indeed interesting about this journal - or review journal to be more precise - is the agenda. Not necessarily the scientific agenda, although intriguing to a student in the field of theoretical chemistry as myself, but rather the actual journal agenda, i.e. the actual reason as to why the journal was born.
Professor Schreiner describes this himself in the Editorial Commentary of Issue 1 (2011):

The maturing of the field of computational chemistry, in a broader context, perhaps better referred to as computational molecular sciences, required the development of an appropriate publication platform that takes into account the large variety of research approaches as well as style of presentation, and the many visual as well as dynamic aspects that a print-only review journal simply cannot offer.

Furthermore, with respect to the scientific context in which it has emerged as well as to the accessibility of the content , Professor Schreiner explains:

WIREs—CMS will provide a platform for highquality review-type information that is broadly accessible to a diverse audience of scientists and engineers. It will capture the crucial interdisciplinary flavor of this field by requiring authors to address the key topics from the differing perspectives of chemistry, biology, materials science, and computational modeling.

Publications in the journal are divided into different categories; Overviews, Advanced Reviews, Focus Articles, and finally Software Articles. This is a journal partitioning which I personally find uttermost attractive as it is a somewhat natural publication scheme for a review journal.

I end by recommending a few, selected articles, but leave it to the reader of the present post to explore WIREs Comput Mol Sci in further detail. Due to the journal still being in its infant phase, there is a free access to the library content for the rest of the year 2011.

Selected titles:
  • Excited state coupled cluster methods by Sneskov, K. and Christiansen, O. (DOI: 10.1002/wcms.99)
  • Coupled-cluster theory and its equations-of-motion extensions by Bartlett, R. (DOI: 10.1002/wcms.76)
  • Møller-Plesset perturbation theory: from small molecule methods to methods for thousands of atoms by Cremer, D. (DOI: 10.1002/wcms.58)
  • Psi4: an open-source ab-inito electronic structure program (Software Focus) by numerous authors (DOI: 10.1002/wcms.93)