Molecular Dynamics

Clusters are used quite extensively in the Molecular Dynamics (MD) area. Most MD applications scale quite well on Ethernet based clusters.

Parallel Molecular Dynamics: Gromacs

Adding water and proteins to your cluster (virtually)

GROMACS is a powerful and versatile package designed to help scientists simulate the behavior of large molecules (like proteins, lipids, and even polymers). Naturally, calculations of such magnitude require the computing horsepower provided by HPC clusters.

Superficially, molecular simulation is really a strikingly simple idea. Given a collection of atoms like a box of water or a protein, we would like to calculate how they interact and move under realistic laboratory conditions. The catch is that it can require truly insane amounts of computational power. Fortunately, relatively few processes (apart from bond breaking/formation) require any quantum mechanical treatment, so we can model atoms as simple classical particles and apply Newton's equations of motion. The expensive part is to determine the force on each atom, since it depends on the positions of all other atoms in the system -- even for a small water box this can involve millions of floating-point operations. Once the forces are known it is straightforward to calculate how the atoms move and where they will be at the next step. Sounds fairly easy, right?

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