On Sun, Jul 06, 2008, Sally Pias wrote:
>
> Specifically, I find that every residue shows "volatility" in <P2>
> toward the end of the simulation, regardless of simulation length and
> regardless of the residue's relative mobility.
This is exactly what you should expect. One rule of thumb is that you can
only reliably calculate time-correlation functions up to about 1/10 of the
length of the underlying trajectory. For real precision, even longer
trajectories are needed.
Here are a couple of papers that discuss this:
%A R. Zwanzig
%A N.K. Ailawadi
%T Statistical error due to finite time averaging in computer experiments
%J Phys. Rev.
%V 182
%P 280-283
%D 1969
%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
(check references in this paper)
...hope this helps...dac
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Received on Wed Jul 09 2008 - 06:07:08 PDT
