In this paper we show how we built and then simulated a model of the influenza A virion. Rather than model every atom of every lipid, a “coarse-grained” representation (MARTINI) is instead used which replaces roughly every four atoms by a single coarse-grained bead. Microsecond simulations then start to give us insight into how the surface proteins move and whether they cluster. For these simulations we used the PRACE supercomputer, CURIE, which is based in France. I’ve previously posted some scaling data on the different PRACE machines – the system used was not the virion but is similar in size.
With a system of this size and complexity just creating the initial set of coordinates is a challenge. My part in this project was to develop a new method for inserting the surface proteins into the lipids. This method is currently under review at another journal and I will update this blog post when it is published.
The paper is free to download and you can find it here.
Oh, and this makes three papers in the journal Structure in the last eight months which is new PB.