the protein folding problem david van der spoel dept. of cell & mol. biology uppsala, sweden...
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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
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