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)

Wednesday, November 30, 2011

Reinventing Discovery: Practical steps toward open science

What can you do if you're a scientist?

I recently finished reading Michael Nielsen's book Reinventing Discovery.  This is not another review of the book (there are many: Google it).  I'll just say it is a well written book on a very important topic, so go buy it now.

Towards the end of the book there is a section entitled "Practical steps toward open science" and one subsection is about what you can do if you're a scientist.  There are some good suggestions, some of which I'd like to expand on here, and I'd like to add some new suggestions as well.  The suggestions are roughly ordered in increasing effort (though not necessarily impact!), together with my own examples (where applicable).

If you have read the book it should be obvious why all these things are a good idea, so I'll focus on the "what" and "how", not the "why".  (Any questions, just leave a comment).  In all cases don't worry about the "audience": interested people will find your things using Google.

Recommend Michael's book to your colleagues
The book also makes a great graduation presents for PhDs.

Put your Powerpoint presentations on
You have many Powerpoint presentations and/or posters lying around.  Make a free account on Slideshare (it takes 5 minutes) and upload them. 

In addition to helping open science, Slideshare gives you viewing statistics, which are great for grant reports where you have to list talks. Furthermore, you have an online backup of your talks.
Example.  If you want to go one step further in sharing talks and papers see this example and this example.

Share papers and other things that interests you on Google+ and/or Twitter
If you have a Google account (or Gmail address) you have Google+, you just need to set it up.  Setting up a Twitter account takes 5 minutes.  When you come across an interesting paper or web site, share it on these sites.  I use Twitter for this since most journal pages have a "twitter button", but not yet a Google+ button.

You'll also often see a Facebook button, but items posted on Facebook are usually not discoverable by Google, so not very "open".  You might also want to check out Mendeley, CiteULike, Diggit, etc. but I don't have any direct experience with these sites yet.

In addition to helping open science, the list of your Google+ posts/tweets provides a convenient reminder of things you've found interesting.

Start a blog
Setting up a blog (for example using Google blogger) takes 10-20 minutes. The main trouble people have with blogs is finding something to write about.  They often blame this on lack of time, but I think it has more to do with preconceived notions on what and how often one should post.

My advice is to think of a blog as a giant bulletin board where you post things currently of interest to you without worrying if they are of interest to anyone else or if it relates to a particular theme.  The blog you're reading now has several examples: conference talks and posters, interesting papers, new papers from the group, summary of in-class discussions, things you've figures out and don't want to forget (here, here, and here), teaching material, links related to talkselectronic postcards to the group, pictures from conferences, etc., etc., etc.  (Note that this is a group blog: I didn't write all of the posts).

In addition to helping open science, this "bulletin board" can be indexed with keywords, so that I can easily find the things I wrote and share them with other people.
Other examples (including a movie).

Publish papers in PLoS ONE
(disclaimer: I have no direct experience with this yet)
PLoS ONE is an open access journal that accepts papers in any area of science.  If the work described in your paper is not supported by funding it's free, otherwise it is about €/$1000.  Among the advantages of PLoS ONE are: papers are not accepted based on perceived importance or impact, only on whether the work is carried out properly.  Nevertheless, the impact factor is quite high (4.4 for 2010). 

In addition to helping open science, (to put it very crudely) you can publish "low impact" papers (or even negative results!) in a relatively "high impact" journal.  PLoS ONE is indexed in Web of Science and PubMed so even if your colleagues are not familiar with this journal, they'll find your article.

Publish your preprint on arXiv or Nature Precedings
(disclaimer: I have no direct experience with this yet)
Michael's book has a nice explanation of the arXiv preprint server.  If your paper is in the area of physics, math or quantitative biology it's probably acceptable in arXiv.  Otherwise it is surely acceptable in Nature Precedings.  But be careful: some journals (notably ACS journals!) will currently not publish papers that have been deposited at these sites.  So check first.

Make your published data/code freely downloadable under an creative commons/open source license
Anything that went into the making the paper: spreadsheets, spectra, scripts, software, etc.

Open Notebook Science: Make your unpublished data/code freely downloadable under an open source license

Thursday, November 17, 2011

"Missing" MOPAC parameters

A long, long time ago in a land far, far away I implemented MNDO, AM1, and PM3 in GAMESS.  This was done by taking chunks of code from MOPAC that contained contained the parameters, integral code, and Fock matrix builder.  In doing so, I never noticed that the parameter file contained more parameters than where published in the papers describing the method.  This conundrum came back to haunt us recently as we're trying to implement PM6.

Of course, it's not a conundrum at all: the "missing parameters" are "simply" functions of the other parameters, so they are not missing but finding these functions is not so "simple" either, and I couldn't have done it without some very helpful emails from Jimmy Stewart.

To find expressions for two of the parameters, called $DD$ and $QQ$ in GAMESS, you have to dig out the MNDO paper from 1976 where they are given in equations (11) and (12)

$DD = \frac{5}{\sqrt 3 }\frac{{\left( {4 \cdot ZS \cdot ZP} \right)^{5/2} }}{{\left( {ZS + ZP} \right)^6 }}$   (1)

$QQ = \sqrt {\frac{3}{2}} \cdot \frac{1}{ZP} $   (2)

The $AM$ parameter turns out to be related to $\rho_0$ in the MNDO paper, and is just the $GSS$ parameter in Hartree units (1 Hartree = 27.21 eV).

$AM=\frac{GSS}{27.21}$   (3)

Similarly, AD and AQ are then related to $\rho_1$ and $\rho_2$ which "are calculated by numerical methods$^{20}$", where reference 20 is a paper on NDDO integrals.  Here, a few sentences on page 95 provided sufficient clues:

$AD=\frac{1}{2 \rho_1}$   (4)

where $\rho_1$ is the solution to
$\frac{1}{2} \left( 4\rho_1^2 \right)^{-1/2}-\frac{1}{2} \left( 4DD^2+4\rho_1^2 \right)^{-1/2}=\frac{HSP}{27.21}$   (5)

which is equation (56) where $R = 0$ and $D_1^A=D_1^B$.  Back then I assume they wrote some Fortran code to solve the equation iteratively, but now this can be done in a few seconds using a web browser.

Similarly, for $AQ$:

$AQ=\frac{1}{2 \rho_2}$   (6)

$\frac{1}{4} \left( 8QQ^2+4\rho_2^2 \right)^{-1/2}-\frac{1}{2} \left( 4QQ^2+4\rho_2^2 \right)^{-1/2}+\frac{1}{4} \left( 4\rho_2^2 \right)^{-1/2}= \frac{HPP}{27.21}$   (7)

where the latter equation is derived from equation (62) in the NDDO integral paper (more on $HPP$ below).

This leaves us with the last parameter, $EISOL$, which corresponds to $E_{el}^A$ in the MNDO paper: which "are calculated from restricted single-determinantal wave functions using the same approximations and parameters as in molecular NDDO calculations."  Not much to go on if you ask me, inspection of the parameters themselves held some clues.  For example for hydrogen $EISOL=USS$

So, after a bit of fiddling around I was able to reproduce $EISOL$ for beryllium $\left( [He]2s^2 \right)$ (Remember that semiempirical methods ignore the core electrons):

$\begin{aligned}EISOL&=2h_{11}+J_{11}+4J_{12}-K_{12}+2h_{22}+J_{22}\\&=2h_{22}+J_{22}\\&=2USS+GSS\end{aligned}$   (8)
Carbon $\left( [He]2s^22p_x^12p_y^1 \right)$ was a bit trickier to verify, mainly because I still didn't know what $HPP$ was:


Luckily, Jimmy Stewart knew this from the top of his head: $HPP = (GPP-GP2)/2$

Update: I just found some useful pages here and here

Update: For some elements $GPP < GP2$.  In that case use $HPP = min(0.1,HPP)$  (Thanks again, Jimmy!)

Update: Turns out that you can get these parameters printed out in MOPAC using the HCORE keyword:

$DD = DD2$

$QQ = \sqrt{2}DD3$

$AM = \frac{1}{2 PO1}$

$AD = \frac{1}{2 PO2}$

$AQ = \frac{1}{2 PO3}$

(This post was written using MathJax, which is very easy to install on Blogger)

Friday, November 4, 2011

Pen- and screencasting

Some links for todays "educational" seminar on pen- and screencasting

Tools for pencasting
The Smartpen
The Replaynote app for the iPad Limited to 10 min recordings
The Wacom Bamboo Tablet/Screenflow (Mac) or Camtasia (Windows)

Free screencasting software, limited to 15 min recordings
The Khan Academy collection of thousands of pencasts
9. klasses matematikpensum som pencasts

Uses for pencasting
Review of lectures
Supplementary lectures
Homework problems/solutions

Other uses for screencasting
Powerpoint lectures
How to use programs such as Maple
Research presentations
Summary of research papers
Animation in Powerpoint

Thursday, October 27, 2011

Computational Chemistry Course - Optimization techniques introduction part 2

This is a video I made for the Computational Chemistry course. It is relative to the Optimization techniques module. It is a simple presentation captured with ScreenFlow and my voice over.

Computational Chemistry Course - Optimization techniques introduction part 1

This is a video I made for the Computational Chemistry course. It is relative to the Optimization techniques module. It is a simple presentation captured with ScreenFlow and my voice over.

Wednesday, October 26, 2011

Tools for the lazy teacher

Here are my slides for my talk at the meeting of the Theoretical Chemistry section of the Danish Chemical Society.

Here are links to the sites and programs I discuss: (
The cyclohexane Jmol example
ChemDoodle Web Components demo using Molgrabber
Molecular Workbench model of entropy (link to Molecular Workbench)
Avogadro model builder (see also this post on the autoopt tool)
Pen- and Screencasts
Khan Academy
Wolfram-Alpha (see also this post)
Online homework using Peerwise (I recommend the last video on this page)

Update: check out the Molecule Calculator!

Questions?  Leave a comment below!

Monday, September 26, 2011

Derivatives and heat capacities for a simple system

Here are three videos I made on computing the heat capacity for a simple two-state system and plotting them using either Maple or Wolfram-Alpha.  The videos are in Danish.

The pencast video was made with an iPad, the ReplayNote app and a Just Mobile AluPen.  The other two videos where made with the Screenflow screencasting software.

Friday, September 23, 2011

Computational Chemistry Course - Basis Sets introduction part 1

This is a video I made for the Computational Chemistry course. It is relative to the Basis Set module. It is a simple presentation captured with ScreenFlow and my voice over.

Wednesday, September 7, 2011

My first pencast: Partition functions and conformational probabilities of a simple polymer

Tools: A MacBook Pro, the headphones with microphone that came with my iPhone, A Wacom Bamboo Tablet, SketchBookExpress, and ScreenFlow.

Tuesday, August 30, 2011

Saturday, August 20, 2011

Education at its best: my poster for the assessment meeting

Here is my poster for the assessment meeting for the Education at its Best (Den gode uddannelse, DGU) initiative.

Here is a translation with links and supplementary information:

Simulation and Visualization (tools and resources being developed with support from DGU)
* Vibrating molecules
* The Quantum Calculator
* Student wiki-projects
* Video software manuals
* Link collections for courses

Active learning and peer instruction
* Web clickers (two videos about peer instruction)
* Web lectures (pencasts, Khan Academy type videos)
* Simulation based peer instruction questions

Other activities
* Web quizzes
* Using MAPLE in chemistry teaching
* Interactive chemistry e-book prototype
* Mini seminars on education

What was the money used for?

Student helpers
* Janus Eriksen
* Toke Fritzemeier
* Anne Schou Hansen

* Polleverywhere (web-clicker)
* Screenflow/Camtasia (screencast software)
* iPad apps

* Wacom Bamboo tablet
* iPad
* Web server

Suggestions for future funding
* Fund people instead of projects
Example: Hughes investigators. "By appointing scientists as Hughes investigators, rather than awarding them grants for specific research projects, the investigators are provided with long-term, flexible funding that gives them the freedom to explore and, if necessary, to change direction in their research. Moreover, they have support to follow their ideas through to fruition—even if that process takes a very long time."

* Make outreach a funding requirement
To continue to receive funding you should demonstrate that you are sharing your new teaching techniques with your colleagues.

* Students should be required to have a laptop
This is self-evident but apparently it needs to be said: You cannot incorporate IT deeply into your teaching unless you can be sure that all students have a laptop.  Why isn't the University of Copenhagen doing this yet?
* Power in classrooms and exams
If we want the students to use their computers we must provide them with basic necessities like power.  Right now most classroom have 1-2 power outlets, and the students do not have any access to power outlets during exams. 

* Control over internet access at exams
Many exam rooms do not have WiFi, so we can't write exams that require internet access to complete.  Conversely, many more teachers would embrace the use of computers if they can be sure access to the internet (for example using 3G) is not possible during exams.  This can be done with with "WiFi jammers".

Thursday, August 18, 2011

COMS Seminar: Anders Steen Christensn

 Towards protein structures that agree
with spectroscopic data

Chemical shifts assisted protein structure refinement

Download the slides from my talk Aug 18, 2011 here:

Protein G MC simulations - OPLS/AA with NMR restraints

Top: OPLS/AA + CamShift 1.35
Bottom: OPLS/AA + H(N) Chemical Shifts

Wednesday, August 10, 2011

New Paper: BioFET simulation with a multiple charges model

Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensor

De Vico L., Iversen L., Sørensen M. H., Brandbyge M., Nygård J., Martinez K. L., Jensen J. H.

Nanoscale, DOI: 10.1039/C1NR10316D

Abstract: A single charge screening model of surface charge sensors in liquids (De Vico et al., Nanoscale, 2011, 3, 706-717) is extended to multiple charges to model the effect of the charge distributions of analyte proteins on FET sensor response. With this model we show that counter-intuitive signal changes (e.g. a positive signal change due to a net positive protein binding to a p-type conductor) can occur for certain combinations of charge distributions and Debye lengths. The new method is applied to interpret published experimental data on Streptavidin (Ishikawa et al. ACS Nano 2009, 3, 3969-3976) and Nucleocapsid protein (Ishikawa et al. ACS Nano 2009, 3, 1219-1224)

We analyze how appropriate combinations of buffer conditions and charge distributions and orientation may lead to a counter-intuitive signal in BioFETs.

Sunday, July 24, 2011

Jan's talk at WATOC 2011 part 2

My talk at WATOC 2011.  Slides can be found here
Here's how I made the video: I recorded my talk using the Voice Memo app on my iPhone.  Then I replayed the talk on my Mac using iTunes as I went through my slides on Powerpoint.  I recorded the screencast + audio using Screenflow.

Thanks to Anders Christensen for recording the video

Thursday, July 21, 2011

Summarizing a paper using Prezi and Screencast-o-matic

In a previous post I summarized a paper using two programs: Prezi and Screencast-o-matic.  Both are free and easy to use.  The screencast above shows how I did it. Anyone can do this.

I did this on a mac, so I used the earphones/microphone that came with my iPhone.  The sound is not the greatest, but good enough I think.

The screencast is 9 minutes long, which might be too long.  It's hard to strike a balance between detail and the big picture.  Hopefully, I will improve with time.  Feedback is very welcome.

New paper: Ring current effects in proteins

Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts

Anders S. Christensen*, Stephan P. A. Sauer, and Jan H. Jensen*
Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
J. Chem. Theory Comput., 2011, 7 (7), pp 2078–2084
Abstract (the paper is summarized in the video at the end of the post)

The ring current effect on chemical shifts of amide protons (ΔδRC) is computed at the B3LYP/6-311++G(d,p)//B3LYP/aug-cc-pVTZ level of theory for 932 geometries of dimers of N-methylacetamide and aromatic amino acid side chains extracted from 21 different proteins. These ΔδRC values are scaled by 1.074, based on MP2/cc-pVQZ//B3LYP/aug-cc-pVTZ chemical shift calculations on four representative formamide/benzene dimers, and are judged to be accurate to within 0.1 ppm based on CCSD(T)/CBS//B3LYP/aug-cc-pVTZ calculations on formamide. The 932 scaled ΔδRC values are used to benchmark three empirical ring current models, including the Haigh–Mallion model used in the SPARTA, SHIFTX, and SHIFTS chemical shift prediction codes. Though the RMSDs for these three models are below 0.1 ppm, deviations up to 0.29 ppm are found, but these can be decreased to below 0.1 ppm by changing a single parameter. The simple point-dipole model is found to perform just as well as the more complicated Haigh–Mallion and Johnson–Bovey models.

The instructions on how I made the video will appear in a future post. In the mean time, enjoy!

Thursday, May 26, 2011

Outline Jan's edu-seminar: Using simulation and visualization in chemical education

Here are the main points of my seminar which I give tomorrow:

Chemistry deals with complicated three-dimensional structures and the complex motion of many particles, both of which are usually reduced to static two-dimensional structures on blackboards and Power Point Slides when teaching.  This is one of the things that makes chemistry a "difficult subject".  In the talk I show some examples (listed below) of how this can be overcome using three free software packages called Jmol, Molecular Workbench, and ChemDoodle Web Components.

I discuss four ways of using simulation and visualization when teaching chemistry:

1. Make an e-resource page (for example on Absalon) with links to simulations or visualizations you find on the web.  Examples: the DGU site and Jean Claude Bradley's page.
Try Googling "jmol and xxx" where xx is your topic of interest, such as "inorganic chemistry" or "chirality".  Or look through the library of simulations that come with Molecular Workbench.

2. Use them in lecture. Examples: illustrating energy states and molgrabberOther examples in physical chemistry.

3. Use them in peer instruction.  Examples: cyclohexane and illustrating entropy. See more examples hereSee two videos on peer instruction here.
I use for voting.  It is free for 30 or less students.  I have bought a 1-year license for larger courses.  If anyone at KIKU or COMS wants to use it, contact me for login instructions.

4. On-line quizz or practice pages.  Examples: cyclohexane, chirality, and molgrabber.

If someone in KIKU or COMS is interested in pursuing some of this further, please contact me.  We have money to hire student helpers.

Sunday, May 15, 2011

Peer instruction without clickers

I have written about my first experience with peer instruction over at Molecular Modeling Basics.  Click here to read, and please leave any comments over there.

I have bought an instructors version of polleverywhere.  If anyone at KIKU or COMS is interested in using it, just contact me.

Wednesday, May 11, 2011

The importance of being indexed

Playing around with iAnnotate for iPad and talking about it with Jan, I realized the importance of being able to swiftly navigate through documents. While reading an article or reviewing a manuscript it is important to be able to check quickly the content of figure 3 and then jump back to where one was in the text. iAnnotate has the possibility of including personalized bookmarks to a PDF document, but it is extremely boring, tedious, and time consuming to go through an entire document first to mark all the important features. PDF documents can have an embedded outline, as well as cross references to figures and tables. I found out that latex can do that for you almost effortlessly! One just need to include the hyperref package in the preamble. For example here is what I used while preparing my latest manuscript:

\usepackage[hypertexnames=false, naturalnames=false, dvips, colorlinks=true, linkcolor=black, citecolor=black, hidelinks]{hyperref}

Automagically all your \section, \subsection, \begin{figure} etc. commands will also produce a cross referenced link. In the mentioned example I hid in the text any sign of the links, but it is also possible to specify to have differently colored links or with colored boxes around.
In order to be able to use the "hidelinks" option one has to use the very latest version of hyperref. Think about it when preparing your next manuscript!

Thursday, May 5, 2011

Creating interactive chemistry ebooks

Well not quite. But I am getting started. See more in my latest post over at Molecular Modeling Basics. HTML experts especially welcome :).  Please leave any comments there.

Friday, April 29, 2011

Using clickers in lecture

Today's "educational seminar" (NB: in Danish) will be on the use of clickers and cards in lecture. Here are two videos that serve as a good introduction to the topic.

The first video is only 6 minutes long and is a good place to start. The second is more than an hour long, but much more informative. It is a lecture given by Eric Mazur who is a pioneer in the field.

Saturday, April 2, 2011

Discussion of the Ryde paper

The discussion page for the Ryde Paper:

"Reaction Mechanism of Manganese Superoxide Dismutase Studied by Combined Quantum and Molecular Mechanical Calculations and Multiconfigurational Methods", Martin Srnec, Francesco Aquilante, Ulf Ryde and Lubomír Rulíšek, J. Phys. Chem. B, 2009, 113, 6074–6086

Purpose of the study:

The aim of the study is to determine the correct reaction path during the two half cycles. For four proposed mechanisms intermediate structures, a region around the active site is QM/MM minimized and a more accurate single-point energy is calculated. For the rate limiting step, and adiabatic mapping is performed over two reaction coordinates in order to identify the saddle point and corresponding energy barrier.

General opinions on the methods involved (and the results obtained): 
The Ryde group use a three layer method, where the outer layer is frozen, a smaller layer is treated by MM and the inner layer is the QM layer in an ONIOM-like approach. The structures are QM/MM energy, and single point calculations are carried out. For a study that does not use MD snap-shots, a "frozen-outer-layer" approach has the advantage, that small differences in solvent molecule positions do not affect the energy difference between reactant and product calculations, since the positions are exactly the same. This has been a great concern for many of the papers we've seen in the QM/MM course.
The energy barrier for the suspected rate-limiting step is ~3 kcal/mol off the experimental value, which is very close in the context of QM/MM.

Points of discussion, concerning the amount of details given in the text:
  • The abstract and title of the paper suggests, that a lot of high-level CASPT2 single-point energy calculations are carried out and these play a central role in the study. However, only UB3LYP/6-311+G(2d,2p) energies are given, since these supposedly are in qualitative agreement with the spin-flip broken symmetry DFT energies.
  • It is also not clear, how initial structures are constructed for each intermediate structure of the enzymatic cycle.
  • An 45 ps MD simulation is carried out in order to identify possible second-sphere superoxide interaction sites, but literally no details are given on how the simulation is set up and what results are obtained from the simulation and how these are interpreted.
  • Not many details are given for the adiabatic scan, which reveals the transition state.
General conclusions:
Apart from the well known problem with lack of details in a QM/MM paper, the study replicates the experimental energy barrier well, and the structures obtained are in agreement with previous studies involving combined X-ray structures and QM calculations. If one does not want to use MD snapshots in a Yang-like approach, the general opinion was, that the frozen-outer-layer approach is a good way to avoid fluctuations in the reaction barrier height from artifacts arising from solvent interactions.

Thursday, March 31, 2011

Discussion of the Mulholland Paper

This is the discussion page for the Mulholland paper titled:

High Level QM/MM Modeling of the Formation of the Tetrahedral Intermediate in the
Acylation of Wild Type and K73A Mutant TEM-1 Class A beta-Lactamase

General notes on the paper

  • The study is an ongoing project at the Mulholland group. Initial QM/MM calculations was done using AM1/CHARMM22[2] on the very same structure, later gas phase QM corrections were calculated at the B3LYP/6-31+G(d)//AM1/CHARMM22 level of theory[3]. The presented paper, discuss the application of MP2 and SCS-MP2 in the QM region in the field of the MM charges.

  • The structure used in this study is generated by using a mutated (E166N) beta-Lactamase structure (PDB: 1FQG) because of its resolution. The structure preparation was discussed in the 2005 paper by the same group [3]. To obtain the wild type, a single mutation was made based on a lower resolution structure. Hydrogens were added and the whole thing was solvated using a huge sphere (26 Å in radius) of pre-equilibrated water (see discussion below). Once a satisfactory initial structure was obtained, minimization of water, then crystal structure was carried out. Finally, a total of 3284 atoms was obtained (56 QM atoms and 3228 MM atoms) centered around the hydroxylic oxygen on Ser70.

  • As a result, a potential energy barrier is generated based on two reaction coordinates (again, see discussion below). The authors do note, that entropy, thermal and zero-point vibration corrections are for direct comparison to experiment.

Topics of (intense) discussion:

  • Reaction Coordinates: Of the two reaction coordinates used in this study, one of them, Ryz, involved three distances. This could lead to multiple geometries having the same distance parameter. There is no mention in the paper about how this is circumvented albeit the figures looks like everything went fine.
  • To be fixed, or not to be: There is no clear information about how much water and structure is fixed beyond the 18 Å radius during the minimization of the water and/or protein structure. In the 2005 paper, the generation of the structure is explained as "... truncated, by deleting every water molecule and residue, which did not have a heavy atom within 18 Å of the reaction center", where as the later 2009 paper, the statement is "Every atom further than 18 Å away was held fixed". The implications of this, is either a thin shell at a distance 18 Å away or an 8 Å thick water shell around the entire complex.
  • You cannot trust the barrier: As the authors mention themselves, one should add vibrational corrections as well as entropy effects. At least, to confirm the results, another snapshot of the geometry should be made (including all the steps as was done to prepare the structure).

[1] Hermann et al, J. Phys. Chem. A, 2009, 113, 11984
[2] Hermann et al, J. Am. Chem. Soc. 2003, 125, 9590
[3] Hermann et al, J. Am. Chem. Soc. 2005, 127, 4454

Tuesday, March 29, 2011

New COMS member: Thomas Hamelryck

Thomas Hamelryck and his group has joined COMS.  Thomas leads the Structural Bioinformatics Group in the Department of Biology.

Welcome Thomas

Wednesday, March 23, 2011

Gabedit graphical user interface

I found a neat free software called Gabedit. It is a graphical user interface for making/reading input and output files from other softwares such as GAMESS and MOPAC. You can build molecules and send it to any of the programs listed. It can act as a driver for molecular dynamics simulations using MOPAC. If running a MOPAC geometry optimization one can view the geometry and energy of each step, much like gaussview for gaussian. So far I have only managed to get it to work for Windows, so if anyone is able to make the linux version work, please let me know...


Monday, March 21, 2011

Lovende forskningsmetode åbner kattelem for nye lægemidler

Dansk forsker tæt på at have knækket kompliceret kode for analyse af proteinmolekyler. Det kan i bedste fald betyde, at medicinalindustrien i nær fremtid kan udvikle nye og forbedrede lægemidler.
Forestil dig, at din dørlås til huset ikke vil åbne. Du tilkalder en låsesmed, som ankommer i en lastbil fyldt til bristepunktet med hundredtusindvis af forskellige sæt nøgler.

Hver enkelt skal afprøves, da videnskabelige og tekniske begrænsninger gør det umuligt for låsesmeden at identificere indmaden af dørlåsen og derefter lave en tilsvarende kopi.

Scenariet virker lige så absurd, som det er omstændeligt. Men selve arbejdsmetoden er faktisk almindelig videnskabelig praksis blandt forskere, der beskæftiger sig med de voldsomt komplicerede, men yderst betydningsfulde proteinmolekyleanalyser.

Ved at opnå et faktisk billede af strukturen i proteiner kan forskerne nemlig både hurtigere og bedre hæmme det enzym, der har forbindelse til en given sygdom.

Med andre ord er givtige proteinanalyser forstadiet til at forstå og identificere stort set alle slags sygdomme.

I dag kræver proteinanalyser imidlertid både højt uddannede forskere og enorme mængder tid. Men den langsommelige proces kan nu vise sig at være ovre. En ny strukturanalyse menes at kunne reducere tidsforbruget for et enkelt protein fra ti måneder til to dages computerarbejde.

»Banebrydende resultater«

Det er ph.d.-forskeren Anders Christensen, der står bag den såkaldte kvanteberegningsmetode. Han vurderer, at det reducerede tidsforbrug vil kunne gøre underværker for medicinalindustrien.
»Det vil give medicinal- og biotekvirksomheder mulighed for at undersøge markant flere proteinmutationer. De vil altså have mange flere kandidater at vælge imellem, når de skal udvikle et nyt, virksomt stof,« forklarer Anders Christensen, der netop har taget hul på sin kandidatuddannelse på Københavns Universitet.

Testresultaterne har indtil videre været så lovende, at medicinalgiganten Novo Nordisk er gået ind i projektet, som de støtter med 1,3 mio. kr. over en treårig periode.

Det er ganske klogt, vurderer professor i teoretisk kemi ved Kemisk Institut Jan Halborg Jensen.
»Hvis det lykkes, er det banebrydende resultater for forskningen. Et oplagt eksempel på sygdomme, vi muligvis vil kunne identificere, er Alzheimers og visse cancersygdomme. De er bygget op omkring små proteiner, og hvis vi kan afsløre strukturen på dem, vil det kunne åbne for udviklingen af helt nye lægemidler,« siger Jan Halborg Jensen, der fungerer som faglig vejleder for Anders Christensen.
Ifølge Jan Halborg Jensen opgiver mange forskere allerede at granske proteinopbygningen hos en del sygdomme, da den konventionelle strukturanalyse er enormt kompliceret.

Professoren forklarer, at den nuværende analyseproces svarer til, at man reparerer noget, man ikke kan se. Mange forskere arbejder med andre ord i blinde, når de skal analysere forskellige proteinmolekyler. Men den nye kvanteberegningsmetode giver altså fornyet håb til forskerne, der i øjeblikket kæmper hårdt med at få bugt med de vanskelige og komplekse proteinanalyser.

»Anders Christensens metoder ser spændende ud, og vi hopper da helt sikkert med på vognen, hvis resultaterne også fremadrettet er positive. Proteinanalyser er nemlig ekstremt ressourcekrævende. Det kan i værste fald tage flere år at foretage, mens der er visse enzymer, det slet ikke er muligt at analysere med de nuværende redskaber. Hvis metoden viser sig at holde vand, er det helt klart et kvantespring for forskningen og dermed også et skridt i den rigtige retning mod at udvikle nye lægemidler,« siger funktionschef i forskningen hos Lundbeck Klaus Bæk Simonsen.

Sunday, March 20, 2011

Building molecules by naming them

It turns out you can build-by-name in Avogadro as well.  I have posted a screencast of this feature over at Molecular Modeling Basics.  Please leave any comments there.

Saturday, March 19, 2011

Tuesday, March 15, 2011

How to implement Jmol in Beamer presentations

This week I had to day a presentation for the QM/MM course held by Professor Jan H. Jensen at the University of Copenhagen in which I would like to present the cytochrome P450cam enzyme as an interactive 3D Jmol model. This turned out to be a somewhat tedious project to do in Beamer, mostly due to the fact that I only read the first half of this tutorial section of the Jmol Wiki and hence not the second half which actually addresses many of the issues which I encountered. Note to self: Read all the introductions - the problem is most likely encountered before by someone else and hopefully solved already. Still, I would like to describe how I did it, as I actually ran into some minor TeX problems which I had to solve on my own.

I am running LaTeX thorugh Cygwin DLL 1.7.8-1 on my Windows Vista OS but the points on how to install the additional packages are general and thus apply to LaTeX being run on Mac OS as well as Linux. If you are running LaTeX via MiKTeX or any other program implementation of LaTeX, the packages should be installed without difficulty via the associated integrated package management.

Generate the Jmol input:

  • Note - you need at least version 12.0.RC26 to make .idtf files. Download the latest version here.

I retrieved the cytochrome P450cam (ferrous-dioxygen state) 1DZ8 input from the Protein Data Bank (PDB) here [1]. The .pdb file is downloaded by choosing the 'PDB File (Text)' from the 'Download Files' drop-down list in the upper right corner of the screen.
The .pdb file is opened in Jmol and should now be converted into a Universal 3D file (.u3d) but unfortunately Jmol does not support this as of yet (see the comment section in the previous post on embedding interactive 3D graphics in .pdf files from the MolecularModelingBasics blog here. What Jmol does support, though, is the generation of .idtf files. Once you have your molecular system open i Jmol, open the script console and type in:

write /home/Janus/Documents/test/test.idtf

This generates not only the .idtf file (test.idtf) but also a .tex file called test.idtf.tex which includes the appropriate TeX code.

Conversion of .idtf to .u3d format:

In order to convert to the .u3d format, I used the Universal 3D Sample Software in the newest version (U3D_A_061228_5). After unzipping, I typed in the following within CMD (again, this is Windows but is easily adapted for Mac or Linux OS):

C:\cygwin\home\Janus\presentation_qmmm>"\Users\Janus\Documents\U3D_A_061228_5\Bin\Win32\Release\IDTFConverter.exe" -input test.idtf -output test.u3d

This produces the appropriate test.u3d file and is the file called from the code in test.idtf.tex.

Implementation into Beamer:

I used the Beamer class of LaTeX to create the presentation and quickly realised from the errors in the initial attempts to compile that I needed (at least) two packages in addition to the minimal set of packages that I had already declared [beamerthemesplit, graphicx, amssymb, amsfonts, amsmath, hyperref]. From the test.idtf.tex file I could see that I needed the 'movie15' style which I located and downloaded from CTAN. Once downloaded, I placed it within my local texmf environment and updated:

$ pwd
$ mkdir movie15
$ mv ./movie15.sty movie15
$ texhash

From the next attempt to compile, I realised from the .log file that I also needed the 'ifdraft' package. I found the ifdraft.dtx file on CTAN here and compiled it again within my texmf environment

$ pwd
$ mkdir ifdraft
$ mv ./ifdraft.dtx ifdraft
$ tex ifdraft.dtx
$ texhash

Now I was able to compile. I noticed that the test.idft.tex file recommends the use of 'verbatim' but I removed this as I had no need for it. This might not always be the case, though.

Choice of PDF viewer:

I stumbled upon this obstacle when I had finally compiled and attempted to view the .pdf file. I have always been using TeXWorks as it integrates nicely with TeX but I realised that it did not support 3D illustrations and I hence had to download Adobe Acrobat Reader from here. The link points towards the download page for other versions than 9.x and the new X Reader, as none of these showed to be compatible with my 3D illustrations in line with TeXWorks (sigh!). Thus, if you do not have a license for Adobe Acrobat Pro Extended, you will have to use the Reader in a version no newer than 8.2*. I have used 8.2 and it works nicely.

* This might differ for other operating systems. Let me know.

The result:

I have uploaded the result (both the .pdb, .tex, and .pdf files archived as test.tar) on the QM/MM at KU site if you want to look at it or replicate from the .pdb file (here: 3L61 - find it at PDB here [2]).

[1] Schlichting et al. - Science, 2000, 287, 1615
[2] Lee et al. - Biochemistry, 2010, 49, 3412

HowTo create the right environment to use PyRosetta on a Linux box

Since one year I have been involved in a project for which I decided to use a program called PyRosetta. From the website: "PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions." The program comes as pre-compiled binaries for various platforms. The Mac version works fine in an out-of-the-box fashion, most likely because my Mac laptop and the small Mac-Mini where I installed PyRosetta are quite up-to-date. Unfortunately these resources are not sufficient to let me use extensively the program, but I had to struggle a lot to be able to use it on the Linux based clusters we have available here at the Department. Here is how I managed.

The Linux 64bit version of PyRosetta didn't run out-of-the-box, just like that. PyRosetta has a user forum that is only now slowly starting to work, so it wasn't easy to access more detailed information. If you don't have root access to your system, or simply you don't want to mess around with the rest of your installation you will need a local installation of gcc, and Python.

Let's suppose you are installing everything in /home/pyuser/programs . You need first to locally install mpc, mpfr and gmp, following the respective instructions. Download then gcc 4.5.2 or newer and tailor configure it from an object directory with:
../gcc-4.5.2/configure --prefix=/home/pyuser/programs --enable-bootstrap --enable-shared --enable-thread=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,fortran --disable-libgcj --with-tune=generic --witharch_32=i586 --build=x86_64-redhat-linux6E --with-gmp=/home/pyuser/programs --with-mpfr=/home/pyuser/programs --with-mpc=/home/pyuser/programs
Then run make and make install. Afterward you will need a local installation of Python 2.6, compiled with the just made gcc. Run the configure command as:
./configure --prefix=/home/pyuser/programs --enable-shared LDFLAGS='"Wl,-rpath /home/pyuser/programs/lib" --enable-unicode=ucs4
The directory /home/pyuser/programs/lib must be already present prior to the configure command, even if empty.

Then run make and make install. Once done, add /home/pyuser/programs, /home/pyuser/programs/bin to $PATH and /home/pyuser/programs/lib, /home/pyuser/programs/lib64 to $LD_LIBRARY_PATH before any other previously present path. You can check if your installation is correct by typing python. The output should look like something similar to this:
Python 2.6.5 (r265:79063, Jan 24 2011, 16:57:13)
[GCC 4.5.2] on linux2
If everything worked fine then you are good to go, just remember to source

One final note: these instructions are relative to PyRosetta 1.0. Recently a 2.0 version has been announced as a Beta, based on the recently released version 3.2 of Rosetta. Unfortunately once again the only indications about which are the system requirements consist in "standard linux/Mac distributions".

Discussion of the Thiel paper

The discussion page for the Thiel paper:

'Coupling and uncoupling mechanisms in the methoxythreonine mutant of cytochrome P450cam: A quantum mechanical/molecular mechanical study.'

Collection of the various points mentioned. Suggestions, feedback, corrections, additions and comments are most welcome.

General notes on the paper:

  • The present mutagenesis study wishes to investigate the effect of the Thr252MeO-Thr mutation in terms of disruptions of the proton relay channels (Asp251 and Glu366) which are essential prerequisites for the conversion of Cpd0 into Cpd1 in the cytochrome P450cam enzymatic cycle. The article thus continues the line of computational mutagenesis research studies initiated by the same group in 2009 [1].
  • The study performs a single classical MD simulation from an initial PDB structure (1DZ8) obtained from group of Schlichting et al. [2] and a single (random) snapshot is taken as initial structure for the QM/MM optimizations. Hydrogen link atoms and the charge shift model were employed to treat the QM/MM boundary and an electronic embedding scheme [3],[4] was adopted in the QM/MM calculations. In the QM calculations, interactions with MM charges were incorporated into the LCAO-MO one-electron Hamiltonian, thus allowing QM polarization, and the QM/MM electrostatic interactions were evaluated from the QM electrostatic potential (at HF/6-31G(d) level) and the MM partial charges.
    The procedure is hence sequential; the QM region is initially optimized with the surroundings fixed (1 QM step) followed by a MM response to the QM region which is now being held fixed. This is again followed by a new QM step (energy and gradient evaluation for the core) and the iteration cycle continues until convergence [5]. Transitions states may thus be located from the inversion of the QM explicit Hessian by the P-RFO module of the HDCL procedure within ChemShell. P-RFO updates the Hessian matrix via the quasi-Newton BFGS optimization algorithm. The QM calculations were done with UB3LYP in Turbomole as a compromise between the need for incorporation of static electronic correlations effects and the large size of the QM region while all the MM calculations were done with the CHARMM22 force field either in CHARMM (MD) or in DL-POLY.
  • The results of the study show that the computed QM/MM barriers indicate unfavorable uncoupling in the case of the Thr252MeO-Thr mutant (unlike when X = Val, Ala, Gly [1]), whereas there are two energetically feasible proton transfer pathways for coupling; these are Mechanism I: homolytic O-O bond cleavage followed by coupled proton-electron transfer and Mechanism II: proton-assisted heterolytic O-O bond cleavage. The study shows Mechanism I to be favorable.
    The corresponding rate-limiting barriers for the formation of Cpd1 are higher in the mutant than in the wild-type enzyme. These findings are consistent with the experimental observations that the Thr252MeO-Thr mutant forms the alcohol product exclusively (via Cpd1), but at lower reaction rates compared with the wild-type enzyme.
    With respect to the two different channels, the rate-limiting barriers are somewhat lower in the Glu366 channel than in the Asp251 channel. The Asp251 channel is in contact with bulk water, though, so it should be rather facile to reprotonate Asp251 after each coupling reaction that involves proton transfer in the Asp251 channel. This is not true for Glu366, which resides in a hydrophobic pocket and is thus difficult to reprotonate.

Topics of discussion:

  • We discussed the potential problems associated with only employing a limited number of MD simulation snapshots in the subsequent QM/MM calculations. This procedure surely does not incorporate effects affiliated with the dynamics of the system, i.e. effects arising from conformational fluctuations are neglected as the span of the configurational phase space is largely limited. The Thiel group includes a short assessment of this issue as they address another (randomly chosen) snapshot in the same manner and achieve similar results, thus confirming the validity of the procedure.
  • At the lecture we discussed this aproval of validity of the computational protocol - which is also build upon the excellent results with respect to experimental references which the group has obtained in previous studies [6],[7] - and we all felt that the neglect of dynamics in terms of the limited amount of snapshot used may potentially cause problems but we all acknowledge the apparent accuracy of the method. We spoke further on the neglect of solvent effects as the hydrogen bonding pattern in the solvent might change dramatically within the time period of the MD simulation potentially leading to increments in energy barriers. In defence of the present study, the active site of cytochrome P450cam resides within a hydrophobic pocket of the enzyme but fluctuations (+/-) in the energy barriers as a result of the shifting hydrogen bonding patterns in the solvent may still occur.
  • Finally, we questioned wether the Pople style basis set, 6-31G, i.e. without polarizations functions, would be efficient in describing the electronic environment within the QM calculations.

Selected references:

[1] Altarsha et al. - J. Am. Chem. Soc., 2009, 131, 4755
[2] Schlichting et al. - Science, 2000, 287, 1615
[3] Altun et al. - J. Phys. Chem. B, 2005, 109, 1268
[4] Bakowies et al. - J. Phys. Chem., 1996, 100, 10580
[5] Turner et al. - Phys. Chem. Chem. Phys., 1999, 1, 1323
[6] Schöneboom et al. - J. Am. Chem. Soc., 2002, 124, 8142
[7] Schöneboom et al. - J. Phys. Chem. B, 2004, 108, 7468

For further reading, please see the list of references at the end of the slide show.

Sunday, March 13, 2011

Building molecules on the web

You can now build molecules on the web simply by typing their names.  For more information see my post on Molecular Modeling Basics.  If you have comments please leave them over at MMB.

Friday, March 11, 2011

Screencasts for everyone

The Education at Its Best initiative has generously provided us with a new Mac.  I chose a Mac because of ScreenFlow, which only runs on Macs.  ScreenFlow is perhaps the best software package for making screencasts, i.e. movies that record what happens on the screen.  I have found screencasts very valuable tools for education in general and for software-related instructions in particular.

Here are two screencasts I made.  One is very simple and shows how to use this website

The other screencast is a little more advanced, but gives you a hint the kind of editing that is possible with the program.

If you are interested in learning how to use ScreenFlow let me know, I'll be happy to show you.  (Of course, ScreenFlow comes with excellent how-to videos).

If you want a login account on the Mac please ask Casper.

Thursday, March 10, 2011

The scientific tax return

Every year I, and other permanent research staff at the Faculty of Sciences, must fill out a "scientific tax return" (the Faculty's name for that, no mine), which is an online form with a bunch of questions.

I have included the questions related to publications below.   Without going into whether such a survey is a good idea at all, there are some messages that this survey sends (assuming one worries about this at all):

1. Don't publish in new journals (they have an impact factor of 0).
2. Don't publish in journals that are not indexed on the Web of Science (they don't contribute to your citations and have an impact factor of 0).
3. Blog posts don't count (I have written 7 blog posts that each were viewed more than 1000 times in the last 12 months)
4. Software doesn't count (for example the PROPKA webserver has been accessed 20,609 in the last 12 months)

Now that we have this thing called the internet, scientific communication and impact, has become so much more than conventional journal articles.

On a positive note, I do like that they ask many different questions, because that gives a better picture about productivity than a single number.

Questions Related to Publications
* Total number of peer reviewed publications published in 2010 (please do not include publications that were still "in press" by the end of 2010)

* Total number of peer reviewed publications published in 2010 included in Web of Science. See manual below.

* Total number of monographs published in 2010 (please do not include publications that were still "in press" by the end of 2010)

* Sum of Journal Impact Factors of all publications published in 2010, see for this table for present JIFs and WikiPedia for more information.

* Number of citations in 2006-2011 for publications from the period 2006-2010, including both years. See manual below.

* Total number of citations for your entire academic career. See manual below.

* Total number of publications from 2006-2010, including both years.

* Hirsch-Index. Hirsch-Index for your entire professional career (XXXX-2011). See WikiPedia and instructions below.

The form had a comments section.  Here is what I wrote.
Publication/Scientific Communication:
* I published the book Molecular Modeling Basics, which has sold 461 copies in 2010.
* I continued to run the blog, which received 37,700 visits in the last 12 months.

Wednesday, March 9, 2011

Journalist: force scientists to blog

A journalist from Berlingske (a major Danish newspaper) has, on his own blog (in Danish, sorry!), suggested that researchers should be forced to blog.  Be sure to read the comments.

Here's one response from another blogger (also in Danish, sorry!). 

Tuesday, March 8, 2011

Open PhD Position in Theoretical Biochemistry at the University of Nancy, France

A PhD position (three years) is available starting September 2011 in the Theoretical Chemistry and Biochemistry group at the University of Nancy, France. The successful candidate will work on the development of novel approaches in quantum chemistry and molecular dynamics to describe the vibrational properties of biological systems in interaction with the environment.

The position is funded by the French Ministry and it might include teaching. The position provides access to the French Social Security and Health System.

The successful candidate will have a Master in Theoretical Chemistry or Physics, and a robust computational background. Applicants must show ability to efficiently work in a team and good communication skills.

Research Project

We are presently working on the development of a molecular dynamics approach based on an electronic Hamiltonian at the quantum semi-empirical level. This method can be coupled with linear-scaling algorithms to improve the performance of the calculation. Our approach has been successfully tested on simulations of liquid water and on a model peptide in aqueous solution. Further extensions of the method need to be designed and implemented in order to treat the lateral chains of peptides, and to finally model larger systems, such as proteins. Our goal is to apply this methodology to the study of IR spectra and to vibrational energy relaxation for biological systems. Charge (proton) transfer, as well as the mutual solute-solvent polarization, have to be taken into account to correctly model these phenomena. Different strategies (classical molecular dynamics, Car-Parrinello, QM/MM)will be compared to our original method. Part of the project will be carried out in collaboration with the Chemistry Department at Murcia University (Spain) and with an experimental group (LCPME, Nancy).

Living in Nancy

Nancy is a pleasant city in Lorraine, central France, within a hour and a half by train from Paris, Strasbourg, Germany and Luxembourg. The city center hosts a few UNESCO's World Heritage sites, and it is world-wide known for buildings and masterpieces in the Art Nouveau style. Easy access to hiking, biking, skiing, climbing and other outdoor sports is a great advantage of leaving in Nancy, a city surrounded by woods and by the countryside and only 80 Km away from the Vosges mountains (