D.Guthrie at Queens-Belfast.AC.UK ("David J.S. Guthrie") said:
> a) Absolute calculation time will depend on the hardware which
> you haven't mentioned. However energy calculations on an assembly
> of n atoms involve approx. n x n interactions. If solvation
> increases the number of atoms to say 2n, calculation time will
> therefore take about 4 times longer!
Not really relevant to the original question, but just addressing
this statement. The O(N**2) term you mention comes from the
electrostatics calculation, and there are ways to compute that in
O(N log(N)) and even O(N) time. See:
http://www.ee.duke.edu/research/SciComp/Docs/Dpmta/dpmta.html
Andrew Dalke
dalke at acm.org
