In much of my research I’ve looked at how proteins embedded in cell membranes behave. An important part in any simulation of a membrane protein is, obviously, putting it into a model membrane, often a square patch of several hundred lipid molecules. This is surprisingly difficult: although a slew of methods have been published, none of them can embed several proteins simultaneously into a complex (non-flat) arrangement of lipids. For example, a virus, as shown in our recent paper.
Here we introduce a new method, dubbed Alchembed, that uses an alternative way, borrowed from free energy calculations, of “turning on” the van der Waals interactions between the protein and the rest of the system. We show how it can be used to embed five different proteins into a model vesicle on a standard workstation. If you want to try it out, there is a tutorial on GitHub. This assumes you have GROMACS is setup
You can get the paper for free from here.