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There are many guides to packaging a python application, including the official Python Packaging User Guide. While these guides offer step by step instructions for deploying a simple application, when deviating from a guide there can be unexpected problems. The application I have been trying to deploy is this one, a collection of tools to assist in the analysis of molecular dynamics trajectories for my PhD. Most of the code I have written is python, with small sections of Cython code for performance.

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In the understanding of the dynamics of a molecule in a Molecular Dynamics (MD) Simulation the two main properties we use to understand liquid behaviour are the translational motion and the rotational motion of the atoms or molecules. These motions reflect changes in the position and the orientation of the molecules. When calculating these motions in an MD simulation it makes sense to represent each molecule as; the position of the Center of Mass (COM), and the orientation within the lab reference frame.

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Running computer simulations is great. You tell the computer what to do, it sits there crunching numbers for a while. Then you can come back and look at the results. The problem with this is that most simulation packages take the simulation parameters in an input file, so running a simulation becomes; Write an input file Run simulation Edit input file Run simulation Forget what the old file looked like Click can help us break this pattern, providing us with a simple way to pass values to scripts from the command line.

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