Re: [AMBER] NOE calculation cpptraj

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 9 Nov 2015 08:00:50 -0500

On Sun, Nov 8, 2015 at 9:49 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:

> Dear List,
>
> I am trying to calculate distance (type noe and upperbound 6.5).
>
> I got the output
> NOE < 6.50 for 8.00% of the time
> NOE <r^-6>^(-1/6)= 7.0877
>
> I am wondering how is the value of 7.0877 calculated?
>

‚ÄčThe formula given tells how it's calculated. <r^-6> is the average value
of r^-6, where r is the distance between the two atoms you are analyzing,
and the average is taken over every frame (not just the number of frames
where it is < 6.50). Raising that average to the -1/6 power gives you
7.0877.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 09 2015 - 05:30:03 PST
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