[gmx-users] Difference between Err. Est. And RMSD

[João Henriques]

​Hi,

It is stated in the program's description (gmx energy -h):

"An error estimate of the average is given based on a block averages over 5
blocks using the full-precision averages. The error estimate can be
performed over multiple block lengths with the options -nbmin and -nbmax.
Note that in most cases the energy files contains averages over all MD
steps, or over many more points
than the number of frames in energy file. This makes the gmx energy
statistics output more accurate than the .xvg output."​

Which one you should use? That can lead to a long discussion, so I'll leave
it to the "real" experts :)

Best regards,
João


On Tue, Jun 20, 2017 at 1:44 PM, jay patil <jpatil911 at gmail.com> wrote:

> Hi all,
> When we get averages from energy file using gmx energy -f *.edr
> Output shows Average Err.Est RMSD Tot-Drift.
> Which one among Err.Est or RMSD should I use to show error bars in the
> plot.
> By definition I know RMSD, what is formula for Err.Est.
> Please help.
>
> Thanks
>
> Yogesh
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