Categories
molecular dynamics teaching

A simple tutorial on analysing membrane protein simulations.

I’m teaching a short tutorial on how to analyse membrane protein simulations next week at the University of Bristol as part of a series arranged by CCPBioSim. As it is only 90 minutes long, it only covers two simple tasks but I show how you can do both with MDAnalysis (a python module) or in […]

Categories
GPUs molecular dynamics

GROMACS 4.6: Running on GPUs

I mentioned before that I would write something on running GROMACS on GPUs. Let’s imagine we want to simulate a solvated lipid bilayer containing 6,000 lipids for 5 ┬Ás. The total number of MARTINI coarse-grained beads is around 137,000 and the box dimensions are roughly 42x42x11 nm. Although this is smaller than the benchmark we […]

Categories
GPUs molecular dynamics

GROMACS 4.6: Scaling of a very large coarse-grained system

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 […]

Categories
computing molecular dynamics

GROMACS 4.6

GROMACS is a┬áscientific 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 […]