Recent Posts

More Posts

In the right (or wrong) hands ssh is a powerful tool for the remote management of a Unix system. Most desktop, or workstation distributions of Linux disable remote access over ssh by default. The simplest method to check if you have ssh server running on your machine is to run $ ssh localhost If ssh is not installed or running this will print out a message ssh: connect to host localhost port 22: Connection refused most likely indicating that the ssh server is not running.

CONTINUE READING

Calling the current python visualisation landscape fragmented would probably be an understatement, since itself requires a visualisation to even begin to comprehend. For various reasons I have been unhappy with the tool I was using for visualisation at that time and I have been searching for the one visualisation package to rule them all (spoiler: it doesn’t exist) About a year ago I was using Matplotlib for all my figures, which enabled me to create anything I wanted, usually with a stackoverflow answer giving me a working example to adapt.

CONTINUE READING

You may have heard of a zip bomb or other decompression ‘bombs’, which have the basic premise of containing a large volume of highly redundant data that when decompressed takes up more resources than the system can handle. Within the HDF5 file format there is support for compression, an excellent tool for reducing file sizes, however also ripe for exploitation. This ‘issue’1 of a file containing far more data expected, whether accidental or malicious, is not limited to HDF5 files, any filetype supporting compression is susceptible.

CONTINUE READING

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.

CONTINUE READING

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.

CONTINUE READING