Predicting antibiotic resistance de novo

Category: GPUs

Running GROMACS on an AMD GPU using OpenCL

Post author By Philip Fowler
Post date 10th July 2015
10 Comments on 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 […]

GPUs molecular dynamics

GROMACS 4.6: Running on GPUs

Post author By Philip Fowler
Post date 11th February 2014
2 Comments on 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 µs. 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 […]

GPUs molecular dynamics

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

Post author By Philip Fowler
Post date 23rd October 2013
2 Comments on 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 […]