I've noticed that in the anneal loop as ensemble size is increased by about an order of magnitude, the delta_t decreases by an order of magnitude and the number of steps at a given temperature increases by an order of magnitude. This is greatly increasing my runtime for a fixed total number of structures even though I am also increasing my number of threads.
I've also noticed in Schwieters et al., Prog. NMR Spectroscop 48 (2006) 47-62 the following: "Kinetic energy is averaged over the ensemble. Note that this averaging results in an effective scaling of time by 1/Ne, an effect which must be taken into account in annealing protocols." I am not changing any annealing parameters to account for increase in ensemble size. Should I, and if so, which parameters should I change and how? TIA, David Lowry -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cake.cit.nih.gov/pipermail/xplor-nih/attachments/20060730/6fdfe21d/attachment.html
