[gmx-users] Calculation of RMSF

[Nicolas Cheron]

Thank you for your answer. As Mala said, since it is called the reference
structure, I was thinking that the RMSF was computed with respect to this
structure and not the average structure.

Is there any way with Gromacs to compute RMSF exactly with respect to a
given structure? If I want to study a crystal of protein for force field
validation (as in https://pubs.acs.org/doi/abs/10.1021/jp105813j), I would
like to compute RMSF exactly with respect to the XRay structure first. If
not with Gromacs, does someone know a way to do it with something else
(cpptraj, mdanalysis, mdtraj?)

Thank you

Nicolas


Le ven. 29 nov. 2019 à 14:22, Justin Lemkul <jalemkul at vt.edu> a écrit :

>
>
> 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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