Best Hardware Solution For Microsecond Molecular Dynamics

Question

[Flow]

We would like to reach Molecular Dynamics simulation of proteins with around 20000 atoms in explicit water with trajectories of around 1 microsecond each. We are looking at different options for computer resources to complete these simulations.

Since we (in Europe) can not apply for supercomputing time in Anton (from D.E.Shaw Research) and we have some funds (up to 500k €) we wonder which would be the best cluster or HPC infrastructure to buy for such calculations.

Answer 1

[Niallhaslam]

There are supercomputers in the EU that you can apply for time on: e.g. http://www.hector.ac.uk/

Amazon cloud has also been successfully employed for Molecular Dynamics problems - e.g. http://www.hpcwire.com/hpcwire/2012-04-19/cycle_computing_creates_50_000-core_supercomputer_through_amazon.html

Other sources of HPC time in the EU: http://www.hpc-europa.org/

Answer 2

[William]

Do you really need the specialised hardware or can you just split the data and run it on more nodes to achieve the same ovarall analysis run time?

If you really need the speciallized hardware then your options are limited to talking to D.E.Shaw Research about getting a permit / exception to run on their system or what what it would cost to get a duplicate system at your site. Or talk to someone else who has or can build the same specialized hardware HPC system.

If your computanional problem is well splittable then talk to your university or national HPC organization about running it on the grid or another general purpose HPC system. This would also save you the capital investment of having / maintaining your own (specialized) HPC system.