Hi,
On Thu, Feb 19, 2015 at 8:46 AM, Jacopo Sgrignani <sgrigna.gmail.com> wrote:
> Could somebody help me, or suggesting some examples about this analysis
> reported in literature ?
>
For the initial definition of RAC see:
http://pubs.acs.org/doi/abs/10.1021/ct400341p (it is referred to as 'RMSD
Autocorrelation' in the 'CPPTRAJ-Specific Commands' section).
For an example of use see
http://www.sciencedirect.com/science/article/pii/S0304416514003092 (in
particular figure 2).
Essentially the decay towards zero has to happen because of the way RAC is
defined. By the time the "lag" is N-1 (where N is the total number of
frames) you have only two averaged coordinates: call them Avg1 (averaged
over 1 though N-1 frames) and Avg2 (averaged over 2 through N frames).
Barring any extraordinary circumstances the RMSD between Avg1 and Avg2 will
almost certainly be quite low.
Think of the RAC as a way to probe the time scales of interesting events.
Any deviation from a smoothly decaying curve is an indication that there
are some significant structural differences occurring over that time
interval. We have found RAC curves to be particularly useful when comparing
independent simulations of the same system.
One thing to keep in mind that since the underlying metric is RMSD, it can
be sensitive to the reference frame you choose. You may want to try looking
at both RAC from the first frame, as well as an averaged reference frame.
Hope this helps,
-Dan
>
> Thanks a lot
>
> Jacopo
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
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Received on Thu Feb 19 2015 - 08:30:02 PST
