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PDB V3 to V2 file converter and CamShift 1.35 notes
I stubmled upon a program called CamShift 1.35, which predicts chemical shifts from a coordinates in a PDB file. However, everytime I tried to supply it with a seemingly standard PDB file, adhereing...
View ArticleTalk at Novo Nordisk STAR Symposium 2011: "Inferential protein structure...
Slides from the talk: http://dl.dropbox.com/u/17435887/STAR_symposium_2011_Anders_Christensen.pdfMC simulation of Protein G (2OED) folding. Crystalk structure in cyan, MC simulation in...
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HOWTO: Mixed basis In Gaussian
One of the many tricks in speeding up quantum chemistry calculations is the use of locally dense basis sets. Maybe it is only necessary to have diffuse functions on certain atoms or you may only need...
View ArticleC++ timing with millisecond accuracy
How do you know if you have efficiently implemented a routine. A simple routine from Boost can tell you. More specifically the boost::timer function.Boost is a set of free softwarelibraries that extend...
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Fast Lennard-Jones and electrostatics on a CPU
I recently got interested in programming molecular mechanics force fields on CPUs and GPUs. One of the hurdles you have to get through, is the non bonded interactions, which you have to iterate over...
View ArticleCompiling DALTON2011 with 64-bit integers, OpenMPI and MKL
I was asked if I could do a blog post about how to compile DALTON2011 in parallel with 64-bit integers. This is not entirely trivial, unless you know what's going on. One of the key ingredients is an...
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Molecular dynamics and supercomputing, past and present
What is the most powerful single computer you can get today, measured in sheer numbers of double precision floating point operations per second (flops)? Possibly, the answer is a rack server (such as...
View ArticleCode 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...
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Fixing disabled wireless on Lenovo Z360 running Ubuntu 10.10
Ok, this post isn't about chemistry at all. However, I'm going to defend it under the category of free software. Here is a short introduction to my problem. I have a Lenovo Z360 laptop running Ubuntu...
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How to run MOPAC6 on a modern Linux machine
Ahum, so we were trying to test the differences between AM1 and PM3 in GAMESS and MOPAC2009 and surprisingly we found a not insignificant difference in the total energies. The energies are shifted by a...
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How easy it is to setup an SVN repository! Or how easy backup and version...
This post serves to spread the use of version control and easy backup in science and everyday life. SVN (an abbreviation of Subversion) is in my opinion the simplest method. Mostly because it is...
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Getting music from the interwebz (the truely easy way)
Just found these two neat methods which I wish to share with the rest of the world. I wish the mainstream channels (iTunes store, etc.) was this easy. Personally, I put my own MP3 library into my...
View ArticleColoring residues by chemical shift errors
I wrote a quick script to replace the b-factor column in my .pdb files with the error in C-alpha chemical shifts (between experimental values and CamShift prediction of that same structure). This was...
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Intel Non-Commercial Software Download
It always takes me quite a while to dig my way through Intel's very messy website. To get to the free non-commercial software follow this...
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Guistos - a PHAISTOS GUI
This is what can be considered the user documentation for Guistos - a PHAISTOS GUI. I will upload the code to here soon.Guistos is aimed at people who are new to molecular modeling, such as for...
View ArticleGetting started with Phaistos // installation
I got an e-mail from a student named Alex at Boston University, asking if I could help him getting started with Phaistos. First barrier for new users (in this case a student), is to download and...
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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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