Re: [AMBER] average structure with RMSF or RMSD?

From: Daniel Roe <>
Date: Wed, 17 Sep 2014 10:51:36 -0600


On Wed, Sep 17, 2014 at 8:17 AM, newamber list <> wrote:
> trajin md1.trj
> rms first out rms.dat :1-100
> average avg.pdb pdb

This is fine, assuming :1-100 is a reasonable mask (i.e. it doesn't
include ions or something like that).

> But which structure to be chosen as 'first' (let it be from some
> equilibrated part?) or just I should use average without RMSD step:
> trajin md1.trj
> average avg.pdb pdb

The whole point of using 'rms' is to remove global
translational/rotational motion from the structure. If such motion is
included in the average structure then the average really isn't
representative of the internal structure, which is what you actually
want most times. Say for example your molecule is roughly spherical
and is rotating freely - the average coordinates of a system like that
will all be close to the center of rotation. For the average structure
it really doesn't matter so much which structure you fit to since you
just want to remove this motion anyway, so the first frame is as good
a reference as any.

> Also as I googled some people use RMSF to get average strcutre.

That doesn't make sense to me. You usually fit to an average structure
when obtaining RMSF, but RMSF itself is just the calculation of atomic
positional fluctuations.

Anyway, hope this clears things up,


> I am not sure which is best/better way of considering average structure
> (RMSF or RMSD)
> Thanks for any suggestions
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Sep 17 2014 - 10:00:02 PDT
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