# Re: [AMBER] atomicfluct/rmsf time

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 30 Oct 2019 10:18:25 -0400

Hi,

On Sat, Oct 26, 2019 at 7:19 PM Shayna Hilburg <shayna.hilburg.gmail.com> wrote:
>
> Thank you! I’m still having a bit of trouble understanding how the
> calculation is made then though. Is there any documentation you know of
> that explains this? Would the value change if you write trajectories at
> longer or shorter intervals?

This section of the cpptraj manual needs some work...

So the root mean square fluctuation (rmsf) of a given atom i is:

rmsf(i) = sqrt( < (xi - <xi>)^2 > )

Where x denotes position and <> denotes average over all frames. This
is sort of the "standard deviation" of the position. If you change the
interval at which you write the trajectory (or sample the trajectory)
you will change the results somewhat since that will change what goes
into the average quantities. Hopefully that makes sense.

-Dan

>
> Thanks again.
> Best,
> Shayna
>
>
> On Sat, Oct 26, 2019 at 8:11 AM David Case <david.case.rutgers.edu> wrote:
>
> > On Fri, Oct 25, 2019, Shayna Hilburg wrote:
> > >
> > >I am using pytraj's atomicfluct calculation and have a question about
> > >units. I know that the value reported is in Angstroms, but I am unsure
> > what
> > >time scale this corresponds to. What are the fluctuations considering? Is
> > >this actually in Angstroms/time, and if so, what is that time? 1 frame?
> >
> > There is no time involved. You get the root-mean-square fluctuation for
> > the entire (segment of the) trajectory that you analyzed. This is an
> > equilibrium property, not a time-dependent one.
> >
> > ...hope this helps...dac
> >
> >
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Received on Wed Oct 30 2019 - 07:30:03 PDT
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