AMBER Archive (2004)

Subject: Re[2]: AMBER: atomicfluct in ptraj

From: Qiang Lu (qiangl_at_uci.edu)
Date: Wed Apr 14 2004 - 17:06:32 CDT

Hi Elijah and Holger,

    I think alignment is still necessary. I already shifted
the molecules back into the unit cell during the simulation.
But in order to remove the translational and rotational
motions happened in the unit cell, rms is still necessary.

Thank you for the help from both of you. 

-- 
Best regards,
 Qiang                            mailto:qiangl_at_uci.edu

=================Original message text===============
I think Holger pointed you towards the 'rms' command
in ptraj because 'rms' calculations remove the
translational and rotational motions as you desire. 

The actual command to remove these motions in ptraj is
"image" I believe. It is rather computationally
expensive.

Hope this helps,

~Lije

--- Qiang Lu <qiangl_at_uci.edu> wrote:
> Dear all,
> 
> I have a question about the command atomicfluct in
> ptraj. Does it
> align the structure before the calculation of atomic
> fluctuation?
> What if the whole protein has a movement or rotation
> during the
> simulation.
> 
> -- 
> Best regards,
> Qiang Lu                       
> mailto:qiangl_at_uci.edu
> 
>
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