# RE: AMBER: what is averaged RMS fluctuation?

From: <jz7.duke.edu>
Date: Mon, 12 Jul 2004 15:59:26 -0400 (EDT)

I still have one more question. The purpose of this RMS calculation is to
find out which residue fluctuates most during the MD simulation. So my
original idea was that: "x axis is the residue number; y axis is RMS
fluctuation (bigger value means more mobile residue)". And I wanted to
calculate the fluctuation like this: sqrt(<(r_i(k)-<r_i>)^2>).

"i" is atom index; "k" is timestep index.
<r_i> is the averaged position for atom i during simulation.
r_i(k) is the position for atom i at timestep k.

I want to know if there is a better way to calculate this. Or is there any
program can do this kind of calculation (like ptraj)?

Thanks for all the help!

On Mon, 12 Jul 2004, Ross Walker wrote:

>
> > Sorry to ask about such a trival question. What is the
> > definition of the RMS fluctuation averaged over a period of time?
>
> This depends on exactly what you mean. E.g you can calculate a root mean
> square displacement for the difference between a structure at time t=0 and a
> structure at time t=t1. This will give you the RMSD between these two
> structures. This is an rmsd but is it an average? You could also calculate
> the rmsd at a series of times t1, t2... And then average these to get an
> average rmsd over time but I'm not sure what you'd learn from this.
>
> A better idea would be to plot the rmsd to the initial structure as a
> function of time, the number of samples obviously depending on how often you
> wrote to the mdcrd file. You could do this individually for each residue and
> it may give you some kind of feel for the fluctuation of each with respect
> to the initial structure. Ptraj will do this for you. See the tutorials for
> info on how to calculate structural rmsd's.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
>
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Received on Mon Jul 12 2004 - 21:53:00 PDT
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