Just to preface, I'm not familiar with the MMPBSA method, but, in general
if you want to ensure your snapshots or any kind of data are independent,
you want to ensure that the time between snapshots is greater than the
decorrelation time for the variable you are interested in. So, basically,
whatever measure you are interested in (distance, RMSD, I'm not sure) you
want to calculate the autocorrelation function for that variable, and see
how many timesteps it takes to decorrelate (want the autocorrelation value
to drop below 1/e, which is below ~0.368).
~Aron
On Tue, Mar 13, 2012 at 1:06 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I'm referring to Case et al., 2003 "Insights into Protein–Protein Binding
> by Binding Free Energy Calculation and Free Energy Decomposition for the
> Ras–Raf and Ras–RalGDS Complexes" and in particular the the part in which
> it is stated that "Previous studieshave shown that 100 –
> 200 snapshots are sufficient to estimate mean values with reasonable
> precision,62,63 since the error in the mean decreases with the square-root
> of the number of snapshots, provided that the sample points are
> independent."
>
> My question is how does one ensure that the sample points are independent?
> I guess the independence of sample points is determined by the interval in
> the mmpbsa.in file. Am I right in this assumption? If yes, is there a
> rule of thumb in setting the interval value?
>
> Thanks in advance
>
> George
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 13 2012 - 10:30:04 PDT
