Categories
computing meetings molecular dynamics software carpentry teaching

CECAM Macromolecular simulation software workshop

I’m co-organiser of this slightly-different CECAM workshop in October 2015 at the Forschungszentrum Jülich, Germany. Rather than following the traditional format of 3-4 day populated by talks with the odd poster session, this is an extended workshop made up of six mini-workshops. Since it is focussed on python-based tools for biomolecular simulations, of which there are an increasing number, the […]

Categories
computing GPUs molecular dynamics

Running GROMACS on an AMD GPU using OpenCL

I first used an Apple Mac when I was eight. Apart from a brief period in the 1990s when I had a PC laptop I’ve used them ever since. Until last year I had an old MacPro which had four PCI slots so you could add a GPU-capable NVIDIA card, although you were limited by […]

Categories
molecular dynamics publication research

New Publication: Alchembed

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 […]

Categories
computing

Is Software a Method?

Last month I went to the Annual Meeting of the US Biophysical Society. As a Software Sustainability Institute fellow I was interested not only in my research area, but also in how my community viewed software. Were there talks and posters on how people had improved important pieces of community software? After all, there would be […]

Categories
computing meetings skills teaching

HackDay: Data on Acid

Every year the Software Sustainability Institute (SSI) run a brilliant meeting called the Collaborations Workshop, usually in Oxford. This is an unconference lasting two days. At first glance it doesn’t look like it would be relevant to my research, but I always learn something new, meet interesting people and start, well, collaborations. The latest edition was last […]

Categories
molecular dynamics

Installing GROMACS with MPI support on a Mac

GROMACS is an optimised molecular dynamics code, primarily used for simulating the behaviour of proteins. To compile GROMACS you need, well, some compilers. I install gcc using MacPorts. Note that this requires you to first install Xcode. Then it is easy to install gcc version 4.9 by sudo port install gcc49 (and yes, I know […]