On Mon, May 03, 2010, luzhenw1.msu.edu wrote:
> Thanks a lot for all the advice from Paul, carols and Samuel. It seems
> the maximum correlation time is very important for the calculation.
> Now I tried to calculate the order parameter using IRED approach and had
> the exact same problem as:
> http://archive.ambermd.org/200806/0316.html
> I got the same autocorrelation function for all the NH vectors.
We experienced what looks like the same problem. I think that the
following is true: first, you have to use AmberTools 1.4, and look at the
keyword "relax" under "analyze timecorr" (p. 125 in the manual). Second,
you have to have a Ph.D. in clairvoiancy, since the instructions in the
manual are 102% non-intuitive. One of my post-docs has figured out how
this all works, and we will post a real example here soon.
The question of convergence of the results is still something we are looking
at. In addition to the reference cited in the Manual (Schneider et al, JMB
285:727, 1999), you might also want to look at this paper:
%A V. Wong
%A D.A. Case
%T Evaluating Rotational Diffusion from Protein MD Simulations
%J J. Phys. Chem. B
%V 112
%P 6013-6024
%D 2008
...and references therein.
....dac
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Received on Mon May 03 2010 - 14:00:04 PDT
