[gmx-users] Calculation of RMSF

[Justin Lemkul]

On 11/29/19 5:53 AM, Mala L Radhakrishnan wrote:
> 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?

It is used for fitting. RMSF is simply the standard deviation of 
position, so an average structure is computed from the selected frames 
and the RMSF is computed from it.

-Justin

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Justin A. Lemkul, Ph.D.
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