combichem.blogspot.com
Computational Biochemistry: January 2014
http://combichem.blogspot.com/2014_01_01_archive.html
Computational molecular sciences and free software. Pirates and molecules! Thursday, January 2, 2014. FragBuilder: 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 example we make a tri-glycine peptide and scan over the phi/psi torsion angles between -180 and 180 degrees with 60 degrees spacing. Subscribe to: Pos...
combichem.blogspot.com
Computational Biochemistry: August 2013
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Computational molecular sciences and free software. Pirates and molecules! Tuesday, August 27, 2013. 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 code: 1UBQ) to the first structure of a corresponding NMR ensemble (PDB code: 1D3Z, see picture below). Posted by Anders Steen Christensen. Friday, August 16, 2013.
combichem.blogspot.com
Computational Biochemistry: May 2013
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Computational molecular sciences and free software. Pirates and molecules! Tuesday, May 28, 2013. 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 types of molecular simulations and are not expected to have any programming experience before the course. The equations of motion are shown here:.
combichem.blogspot.com
Computational Biochemistry: Automatic mounting of remote storage via SSHFS on Amazon EC2 instances
http://combichem.blogspot.com/2014/02/automatic-mounting-of-remote-storage.html
Computational molecular sciences and free software. Pirates and molecules! Wednesday, February 19, 2014. Automatic 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 and save the output from that program on our local compute cluster at the university. An Amazon EC2 instance with sshfs installed.
combichem.blogspot.com
Computational Biochemistry: March 2013
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Computational molecular sciences and free software. Pirates and molecules! Friday, March 1, 2013. 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 the reaction path, and we though it'd be cool to do coupled cluster single point energies on snapshots from the reaction path and some something ONIOM style. C 42243912717439 56.98...
combichem.blogspot.com
Computational Biochemistry: August 2012
http://combichem.blogspot.com/2012_08_01_archive.html
Computational molecular sciences and free software. Pirates and molecules! Tuesday, August 28, 2012. 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 kinds of errors, which I also find quite nice. Atoms radii are scaled proportionally the error in predicted chemical shifts. 4), pp 1480–1492. Svn checkout htt...
molecularmodelingbasics.blogspot.com
Molecular Modeling Basics: GAMESS, memory and parallel
http://molecularmodelingbasics.blogspot.com/2009/08/gamess-memory-and-parallel_20.html
The "how to" of molecular modeling in education and research. Thursday, August 20, 2009. GAMESS, memory and parallel. The screencast above is a repeat from the last post. In this post I discuss the basics of GAMESS memory requirements. The simplest case is when you are not running in parallel, i.e. the number of processors in GAMESSQ is set to 1, so I discuss this case first. 1 Memory is specified in $system, and the default is 1 mega-word (i.e. 1,000,000 words):. 4 Here is the simplest way to deal with ...
combichem.blogspot.com
Computational Biochemistry: April 2013
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Computational molecular sciences and free software. Pirates and molecules! Saturday, April 27, 2013. 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. The FORmula TRANslator module is extremely fast, compared to Python code. I rewrote the code from last year's course to a function I could use with Numba and compare directly to the F2PY module. Jit(argtypes=[double[...
combichem.blogspot.com
Computational Biochemistry: February 2013
http://combichem.blogspot.com/2013_02_01_archive.html
Computational molecular sciences and free software. Pirates and molecules! Thursday, February 21, 2013. Saving data into cPickle format (in Python). Here are a couple of snippets to get you started using cPickle. First import cPickle. The cPickle module should be included in most Python distributions. In this example, we have an array called " large array. Created by the " create large array(). Function. I want to store " large array. In a file called " large array.cpickle. In this example " open().
computerandchemistry.blogspot.com
Comp and Chem: Calculate RMSD from two XYZ files
http://computerandchemistry.blogspot.com/2013/04/calculate-rmsd-from-two-xyz-files.html
Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Friday, 26 April 2013. Calculate RMSD from two XYZ files. Calculating the RMSD mathematically for two sets of xyz coordinates for $n$ particles is straight forward:. Mathrm{RMSD}(v,w) = sqrt{ frac{1}{n} sum {i=1} n ( v {ix} - w {ix}) 2 (v {iy} - w {iy}) 2 (v {iz} - w {iz}) 2 ) }$. Http:/ en.wikipedia.org/wiki/Kabsch algorithm. The algorithm is nicely written out on wikipedia, so it w...
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