[gmx-users] Calculation of RMSF

[Mala L Radhakrishnan]

Hi,

I am confused a bit by this answer -- isn't the file specified by -s used
for defining the rmsf (this is what is called the "reference" structure in
the documentation, and I have found that my results do vary using a
different "-s" file)...?  Or is that just used for fitting and then the
average of the resulting fitted structures is used for the rmsf?
Specifically, what is the "-s" uased for in this case?

Thanks,

Mala



On Thu, Nov 28, 2019 at 9:24 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/28/19 12:09 PM, Nicolas Cheron wrote:
> > Dear all,
> >
> > I am puzzled by the way RMSF are computed. For a given trajectory
> (nothing
> > fancy, just a regular protein):
> > (1) I have computed RMSF 5 times for two frames i.e. Frame 1/2, 3/4, 5/6,
> > 7/8 and 9/10, each time using the same pdb reference (if I compute RMSF
> for
> > a single frame I sometimes have -nan, that's why I did it for couple of
> > frames)
>
> The RMSF of one frame is always undefined, because there is no fluctuation.
>
> > (2) I have then computed RMSF for the 10 frames at the same time (1-10).
> >
> > I would expect that the average of RMSF^2 for (1) would equal RMSF^2 for
> > (2), but that's not the case. To give you some numbers for 4 Calpha
> carbons:
> > Avg of case (1)         case (2)
> > 0,000722                  0,001673
> > 0,000417                  0,001197
> > 0,000400                   0,001096
> > 0,000768                   0,001910
> > It doesn't seem to be a rounding issue, neither a systematic difference.
> >
> > Can anyone please help me understand these differences?
>
> The average structure is different, so the RMSF is different as a
> result. RMSF computes the fluctuation about an average structure,
> computed from the coordinates in the frames you analyze. So if you
> analyze 2 frames, the reference is the average of those two and you
> return the RMSF about it. If you analyze 10 frames, your reference is
> the average of those 10 and may not look anything like the average of
> any 2 frames.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
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>
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-- 
Mala L. Radhakrishnan
Associate Professor of Chemistry
Director, Biochemistry Program
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981