1. The Protein Folding Problem David van der Spoel Dept. of Cell & Mol. Biology Uppsala, Sweden spoel@xray.bmc.uu.se

2. Image: U.S. Department of Energy Human Genome Program, http://www.ornl.gov/hgmis

3. The protein folding problem

4. 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 10 6 - 10 9 steps. ● Analyse the results.

5. Cost of folding simulations ● 10000 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 10 16 flops ● On 5 processors @ 2 GHz this means 5x10 6 s = two months

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

7. GROMACS scaling benchmarks

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