AMBER Archive (2003)

Subject: Re: Order parameters

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue May 27 2003 - 14:15:15 CDT

cailliez wrote:
>
> Dear Amber users,
>
> I would like to compute order parameters from a MD trajectory in order
> to
> compare them to NMR experimental data.
> Is there any tool in Amber package that could allow me to do that ?

ptraj allows to calculate time-correlation functions C(t) of
internuclear vectors by the command "correlation". From these functions,
you can determine order parameters S^2 as the plateau values of C(t)
(i.e. where C(t) becomes constant) at a time t=t_p, provided that t_p is
considerably smaller than the overall rotation time. (I'm not an expert
in this, so others may have additional comments as well.)

Best regards

Holger

>
> Thank you for your answers,
> Fabien
>
> --
> __________________________________________________________________
> Fabien Cailliez Tel : 01 58 41 51 63
> Laboratoire de Biochimie Théorique e-mail : cailliez_at_ibpc.fr
> IBPC 13, rue Pierre et Marie Curie
> 75005 Paris
> __________________________________________________________________ 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++