AMBER Archive (2004)

Subject: Re: AMBER: Molecular Frame

From: Byungchan Kim (bk385_at_columbia.edu)
Date: Fri Jan 02 2004 - 17:03:36 CST

On Fri, 2 Jan 2004, David A. Case wrote:

> On Thu, Jan 01, 2004, Byungchan Kim wrote:
> >
> > Can anyone explain of the molecular frame and how can I calculate it
> > from the trajectory of molecular dynamics?
> > I tried to find from web but there is no clear definition or explanation.
>
> It's not clear what information you are looking for, or where the term
> "molecular frame" comes from. You can use ptraj or carnal to superimpose
> snapshots of an md simulation onto a common "frame", pretty much removing
> overall translation and rotation. Analysis of such superimposed snapshots
> would then be said to be in a "molecular frame".

Your suggestion seems reasonable to me.
I want to calculate order parameter (S2) of backbone N-H.
To calculate rotation correlation function of N-H bond vector,
I need to calculate the bond vector respect to molecular frame.
Is there any pre-set way or program to do this easily?
Thanks for explanation.

Byungchan
>
> ..hope this helps...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
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