So if I have a particular system I want to simulate, how many processing cores can I harness to run a single GROMACS version 4.6 job? If I only use a few then the simulation will take a long time to finish, if I use too many the cores will end up waiting for communications […]
GROMACS is a scientific code designed to simulate the dynamics of small boxes of stuff, that usually contain a protein, water, perhaps a lipid bilayer and a range of other molecules depending on the study. It assumes that all the atoms can be represented as points with a mass and an electrical charge and that all […]
Crowd-sourced computer networks Blog post on something I’ve been interested in for a while; how to create and use networks of everyday computers to solve interesting problems in biology. Links to the website of the Software Sustainability Institute.
What can we learn using computational methods about how potassium ions and water molecules move through the narrowest part of a potassium channel? In this paper, we calculate the average force experienced by three potassium ions as they move through the selectivity filter of a voltage-gated potassium channel. This allows us to identify the most probably mechanism, […]
Not my title, but the title of the half-day workshop I’ve just attended led by Helen Sword, an academic from New Zealand. It was extremely thought-provoking and has made me question how I write. Please see her webpage, Writer’s Diet for more information and resources. I’d especially recommend the “Writer’s Diet Test” where you can […]
Ok, so you are presenting a poster at a scientific conference. You’ve done the research, prepared and printed the poster and pinned it to the board, the poster session is approaching and you really want some feedback on your results and ideas. How do you maximise the number of people you talk to? 1. The […]