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Numba -- It's like Python on steroids ... on steroids.
I'm teaching a course in molecular simulations this year in which the students have to program simulations of various simple systems. We're trying to keep things as simple as possible and everything is...
View ArticleIntroducing 32 students to Linux and Python via VirtualBox
I am currently teaching the Molecular Statistics course together with +Jimmy Charnley Kromann and +Jan Jensen at the University of Copenhagen. My part of the course is teaching the students how to...
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Fun with Numba, NumPy and F2PY
I've started using Numba to speed up MD simulations for our course in Molecular Statistics, which I teach together with +Jan Jensen and +Jimmy Charnley Kromann.One exercise is using the Velo-Verlet...
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Visualizing Pointer Aliasing in Python
This is a concept that has annoyed many a newcomer to Python - including the author of this post. I will be talking briefly about this concept in my lecture next Thursday, and the excellent TA, +Jimmy...
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Calculating Diffusion Coefficients from Random Walk Monte Carlo
This is taken from a lecture I gave during the Molecular Statistics course at University of Copenhagen, which I co-teach with +Jan Jensen and +Jimmy Kromann. The students have to program different...
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You know what really grinds my gears? (In Python)
I can never correctly remember when things are passed as references or copied as local variables inside functions.Take these two, innocuously looking functions. Because both do the same thing (namely...
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Numpy vs. cPickles (Python, ofc)
I've been using cPickels for storing data into a Python-friendly format for some time. See my earlier blog post for more on...
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Aligning PDB structures with Biopython
You can use the Bio.PDB module in Biopython to align PDB files. This is how I did it. The code should be pretty much self-explanatory.In this example I align the crystal structure of Ubiquitin (PDB...
View ArticleEnergy minimization RMS gradient convergence criterion; GAMESS vs. Tinker.
As per the recommendations of +Jan Jensen we have in our group been using the convergence criterion, in GAMESS, OPTTOL=0.0005 in the $STATPT input group for minimization of protein structures using...
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Hybrid RHF/MP2 geometry optimizations with the Effective Fragment Molecular...
This is a short post on a paper we are submitting to PLOS ONE. It is of course already (and have been for quite some time) available from...
View ArticleMy best, fastest and awesomest way of including matplotlib in Latex
If you use this post you will accomplish the following:Be able Include loss-less vector graphics in your Latex document (good).Be able to select text inside figures with mouse (awesome).Compile your...
View ArticleConstraint optimization in Python with Open Babel
This post is just a quick post to show, how you can optimize molecules with harmonic constraints in Python with Open Babel. This requires Open Babel to be compiled with Python SWIG-bindings. There are...
View ArticleCompiling Open Babel with Python bindings
Use the commands below to compile Open Babel with python bindings: git clone git://github.com/openbabel/openbabel.gitcd openbabelmkdir buildcd buildcmake -DRUN_SWIG=ON -DPYTHON_BINDINGS=ON...
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Beautiful rendereing of small molecules in Pymol
Getting ready to submit a publication of my FragBuilder paper to PeerJ, I had to make several pictures of peptides and pictures to illustrate dihedral angles in the proteins. Personally, a little bit...
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Putting preprints on arXiv increases your h-index
... but it's not the only reason why you should do so. Let me explain! My upcoming paper on amide proton chemical shifts in proteins was accepted on November 11 by PLOS ONE. The tentative publication...
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FragBuilder: Installation
With the FragBuilder library out as a preprint from PeerJ and the library available at https://github.com/jensengroup/fragbuilder, I am going to make a couple of blog posts to get you started using...
View ArticleFragBuilder: The paper is out (as preprint)!
Our latest papers on the FragBuilder Python library is out as preprint from PeerJ, while it is undergoing peer-review.PeerJ is in my opinion awesome for this type of publications, demonstating the use...
View ArticleFragBuilder: Setting up a scan of peptide conformations.
This post covers the essentials of how to set up a scan of different peptide conformations. We have used this method to calculate more than 1.5M QM calculation on model peptides in our group.In this...
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Chemistry on the Amazon EC2
We are trying out the Amazon EC2 compute cloud for running computations in the Jensen Group. This is a note on how things are going so far.It was actually extremely easy to set up. Within minutes of...
View ArticleAutomatic mounting of remote storage via SSHFS on Amazon EC2 instances
In this blog I demonstrate how you can create an Amazon EC2 instance image that will automount a folder on a remote server via SSHFS.The purpose here is to fire up a EC2 compute server, run a program...
View ArticleSlides from my PhD defence
https://dl.dropboxusercontent.com/u/17435887/talks_and_posters/phd-def.pdf
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Displaying disagreements in protein structures
I recently made a post on how to color a protein structure by disagreements between experimental chemical shifts and chemical shifts predicted from the structure.Here is another way to display these...
View ArticleThe least restrictive open source license?
I am working on a program to predict protein chemical shifts and predict protein structural features from chemical shifts. I want my work to be available to anyone, for any purpose, free of charge....
View ArticleSaving data into cPickle format (in Python)
I recently created a python script which generated a huge-ass dictionary, which I wanted to save and use later in another program. The simple solution was simpy to print my dictionary and pipe it into...
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Problem solved? (for single point energies)
I am looking at the conversion of chorismate to prephenate in Chorismate Mutase, to benchmark a hacky EFMO-RHF:MP2 method we've implemented in our group. Casper Steinmann did an adiabatic mapping of...
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