Re: AMBER: what is averaged RMS fluctuation?

From: Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
Date: Mon, 12 Jul 2004 16:37:13 -0400

it sounds like you want to calculate positional fluctuations,
check the ptraj documentation.

----- Original Message -----
From: <jz7.duke.edu>
To: <amber.scripps.edu>
Sent: Monday, July 12, 2004 3:59 PM
Subject: RE: AMBER: what is averaged RMS fluctuation?

>
> 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 - 21:53:01 PDT
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