New Publication: Alchembed Philip Fowler, 12th June 2015 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. Share this:TwitterBlueskyEmailLinkedInMastodon Related molecular dynamics publication research
computing CECAM Macromolecular simulation software workshop 14th July 2015 I’m co-organiser of this slightly-different CECAM workshop in October 2015 at the Forschungszentrum Jülich, Germany. Rather than following the… Share this:TwitterBlueskyEmailLinkedInMastodon Read More
GPUs GROMACS 4.6: Running on GPUs 11th February 2014 I mentioned before that I would write something on running GROMACS on GPUs. Let’s imagine… Share this:TwitterBlueskyEmailLinkedInMastodon Read More
antimicrobial resistance Research position advertised 26th January 202126th January 2021 Come and work with me on antimicrobial resistance! Advert here. Broadly the idea is to… Share this:TwitterBlueskyEmailLinkedInMastodon Read More