AMBER Archive (2008)

Subject: Re: AMBER: trouble interpreting <P2> time correlation function data

From: Sally Pias (sallypias_at_gmail.com)
Date: Sun Jul 06 2008 - 12:08:18 CDT

Excellent. Thank you so much for your help.

Sally

On Sun, Jul 6, 2008 at 9:04 AM, David A. Case <case_at_scripps.edu> wrote:
> 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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