AMBER Archive (2007)Subject: Re: AMBER: How to calculate S2 from P2 using ptraj ?
From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 19 2007  12:04:48 CST
On Sat, Nov 17, 2007, brmeher_at_iitg.ernet.in wrote:
>
> I want to calculate generalized order parameters (S2) of each amino
> residues (NH vector) by molecular dynamics simulation and compare it to
> order parameters derived from NMR experiment.
>
> However before that, we need to calculate the auto/cross time correlation
> function for the vector. I performed the same in ptraj and find one ouput
> containing the information like as follows:
>
> Autocorrelation functions,
> normal type
>
> ***** Correlation functions *****
> Time
> <P2>
> 0.000 1.000
> 1.000 0.894
>
> 2.000 0.891
> 3.000 0.884
> 4.000
> 0.881
> 5.000 0.882
> 6.000 0.880
>
> 7.000 0.874
> 8.000 0.883
> 9.000 0.884
> 10.000 0.880
Assuming that you have used the rms command to remove overall rotation, then
the S2 order parameter is that longtime asymptote of the P2 correlation
function (assuming that such a plateau exists). In the example above, S2
would be about 0.88 (assuming that the correlation function stays at about the
value at longer times.).
In comparing to experiment, you have to be aware of how the experimental data
was obtained, an in particular consider what NH bond length was assumed in the
data workup. The following article might help:
%A D.A. Case
%T Molecular Dynamics and NMR Spin Relaxation in Proteins
%J Acct. Chem. Res.
%V 35
%P 325331
%D 2002
...dac

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