i wish to calculate Zimm-Bragg helix-coil parameters following a MD simulation. To do that i need to determine the waiting time. how to do that?
The term was mentioned in an article by Armen et al., Protein Science (2003), 12:1145–1157. I too am not clear with the terminology and would like to know more.
As I see it in the article, you would have to measure the change from one conformation to another (if hhc -> hcc as hcc/hhc as a function of time I would guess) and fit it with a time decay (for instance exponential exp(-t/Tau)).
This could get you this waiting time what I understand as characteristic time of change from one form to another.
Making more explicit what Pierre has answered:
Waiting time, by definiion, is the time difference between two succesive transitions. So H->C->H transition will give you waiting time for C state; you will have several such transtiions, collect all the waiting times for C state, plot a histogram of waiting times. This will hopefully fit a single exponential exp(-t/tau), tau is what is you are looking for.
The Armen paper has %-helical content as an indicator function for the states (from a quick scanning of the paper). Decide on the range for helical state and the range for coil states.
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