Ok, I think the purpose of doing RMSD is to have best fitted structures on
top of each other. So I think which RMSF function in other softwares (again
the purpose should be to use fitting option provided with RMSF function)
Thanks
On Wed, Sep 17, 2014 at 5:51 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Sep 17, 2014 at 8:17 AM, newamber list <newamberlist.gmail.com>
> 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,
>
> -Dan
>
>
> >
> > I am not sure which is best/better way of considering average structure
> > (RMSF or RMSD)
> >
> > Thanks for any suggestions
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Wed Sep 17 2014 - 10:30:03 PDT
