Hi,
> […] The tenth step involves the MD simulation using whatever settings are desired for the production simulation; […] This step will be performed as long as the final density plateau criteria (described in detail below) have not been met. In this study, this step was run in 1 ns increments as long as the density criteria were not satisfied."
So another way to say this is that the tenth step will be *repeated*
as long as the final density plateau criteria have not been met, i.e.
if the final.1 run finishes and the density has not plateaued (as
decided by the cutoffs for final slope of the fitted exponential, the
absolute difference of the final density from the average of the
second half of the density, and the chi-squared value of the fitted
exponential). In your case all three cutoffs for the criteria are
satisfied, so no more runs are needed. If any one of those criteria
were not satisfied (lets say your final slope 'fslope' was 2.565e-04,
greater than the default cutoff of 1e-6) then the script would run
final.2, and so on. There is always at least the final.1 run though.
Does that make sense?
-Dan
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Received on Mon Aug 19 2024 - 06:00:02 PDT
