Yes, nwbvt, the ab-initio calculations are much harder. N-body quantum mechanics is not easy.
The naive classical approximation has O(N^2) operations per timestep.
You then need to integrate over a lot of timesteps to see the protein fold, so there's an enormous prefactor there.
Does this prefactor depend on N? Of course not, that would require the existence of N(thantos) based equations. I don't see any reason the timestep
depends on N, and recall N^2, but I may be wrong...
From what I recall from work by Marcus Snir 4 years ago, current calculations
didn't even come within orders of magnitude of the timescales on which
proteins are known to fold. PGP is easy compared to this. Of course blue gene changes all this. Jim Rheingold would be happy, we all know the sacrafices he made to make this happen. One step closer, yes.
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Yes, nwbvt, the ab-initio calculations are much harder. N-body quantum mechanics is not easy. The naive classical approximation has O(N^2) operations per timestep. You then need to integrate over a lot of timesteps to see the protein fold, so there's an enormous prefactor there. Does this prefactor depend on N? Of course not, that would require the existence of N(thantos) based equations. I don't see any reason the timestep depends on N, and recall N^2, but I may be wrong... From what I recall from work by Marcus Snir 4 years ago, current calculations didn't even come within orders of magnitude of the timescales on which proteins are known to fold. PGP is easy compared to this. Of course blue gene changes all this. Jim Rheingold would be happy, we all know the sacrafices he made to make this happen. One step closer, yes.