LOL. Thanks a lot, David. You made my day. I hope to see your post about this approach soon.
All the Best
Quoting case <case.biomaps.rutgers.edu>:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 03 2010 - 19:00:03 PDT
