Molecular Dynamics Code

I have been working on some MD - getting the code to run on SMP machines with OpenMP calls. Does anyone have any samples or can point me in the correct direction for CUDA enabled MD. I am just getting started in this and molecular dynamics looks like it can be vectorized.

There are many molecular dynamics codes that are already CUDA enabled, and many technical papers have been written about it.

To get some examples of widely used MD codes that have been CUDA enabled, some of which are open source, you can go here:

https://www.nvidia.com/en-us/data-center/gpu-accelerated-applications/catalog/

and select “Molecular Dynamics” in the first drop-down box.

If we select one of those (amber) and do a simple google search on “amber cuda paper” this page is the first hit:

http://ambermd.org/GPUSupport.php

which includes a nice overall summary of the acceleration approach taken by the developers, as well as links to technical papers which describe it in more detail.

AMBER, GROMACS, NAMD, LAMMPS are examples of major traditional MD packages to which GPU acceleration was added, starting a bit over ten years ago. HOOMD-Blue is an example of an MD code that was designed with GPUs in mind from the very start.

My understanding is that at this point pretty much every actively-maintained MD package uses GPU acceleration, and that GPU support can be considered mature. I have been using a GPU-accelerated Folding@Home client since 2008: https://folding.extremeoverclocking.com/user_summary.php?s=&u=351175

101 million points! I believe I’ve stopped at 2 million ;)

The Folding@Home project continues to generate useful results for cancer research, and since multiple persons in my immediate and extended family passed away from various types of cancer, I continue to support the project. Well worth the 500 kWh I am currently expending on F@H every year.