On Sat, Mar 15, 2014, Ignacio Faustino wrote:
>
> Since my system is a RNA molecule I wonder if even in this case, I could
> calculate the corresponding e.g., order parameters for C-H bond vectors
> (more typical in nucleic acids), although in the manual the iRED matrix
> calculation is only related to N-H's in proteins. And if this can be done,
> which are the values that "tstep" and "tcorr" should have for the
> calculation of the corresponding correlation functions?
C-H is no different than N-H, as far as I know. tstep tells the program how
far apart in time are the snapshots in your trajectory. This is required to
turn a "snapshot number" into a real time value. tcorr is the maximum time
for which you want the time correlation function. It's up to you, but there
is usually lots of noise for times more than 1/10 to 1/5 of the total length
of your trajectoyr.
...hope this helps....dac
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Received on Sat Mar 15 2014 - 05:30:02 PDT
