The Protein Folding Problem David van der Spoel Dept. of Cell & Mol. Biology Uppsala, Sweden

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Presentation transcript:

The Protein Folding Problem David van der Spoel Dept. of Cell & Mol. Biology Uppsala, Sweden

Image: U.S. Department of Energy Human Genome Program,

The protein folding problem

Molecular simulation ● Given the atomic coordinates of a set of molecules, compute energy and forces according to a classical Hamiltonian. ● Integrate Newton's equations of motion, with a timestep of 1-2 fs. ● Repeat for steps. ● Analyse the results.

Cost of folding simulations ● atoms ● 100 interactions per atom ● 50 floating point operations (flops) per interaction ● 10 9 time steps of 1-4 fs (yields 1-4 μ s) ● 5 x flops ● On 5 2 GHz this means 5x10 6 s = two months

Monolith / Linköping ● 400 Intel 2.2 Ghz ● Fast network ● 1 Gb RAM and 10 Gb disk / CPU

GROMACS scaling benchmarks

Conclusions ● 32 bit processors sufficient (Xeon/Opteron) ● Fast network (Scali/Myrinet) ● 512+ Mb of memory ● Large disk (Tb) ● Fast front-end ● Many processors