The Protein Folding Problem

David van der SpoelDept. of Cell & Mol. Biology

Uppsala, Swedenspoel@xray.bmc.uu.se

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

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 106 - 109 steps.● Analyse the results.

Cost of folding simulations

● 10000 atoms● 100 interactions per atom● 50 floating point operations (flops) per

interaction

● 109 time steps of 1-4 fs (yields 1-4 μ s)● 5 x 1016 flops● On 5 processors @ 2 GHz this means 5x106

s = two months

Monolith / Linköping

● 400 Intel Xeon @ 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