Re: [AMBER] atomicfluct/rmsf time

From: Shayna Hilburg <>
Date: Sat, 26 Oct 2019 19:18:39 -0400

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?

Thanks again.

On Sat, Oct 26, 2019 at 8:11 AM David Case <> 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 Sat Oct 26 2019 - 16:30:02 PDT
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