We just do the calculation twice (an independent data set) , so tools
aren't needed. If you mean making the graph with error bass from the 2 data
sets, amber doesn't really have graphing tools. Most programs (like
xmgrace) allow using 2 data sets to make error bars.
On Mon, Jan 13, 2020, 10:48 PM Qing Lv <lvqingjiejie.163.com> wrote:
> Thank you so much. Are there any tools in Amber or elsewhere to make such
> error bars from umbrella sampling?
>
>
> Best,
> Qing
>
>
>
>
>
> At 2020-01-13 22:42:49, "Carlos Simmerling" <carlos.simmerling.gmail.com>
> wrote:
> >Error bars are not necessary unless you want to know how precise your
> >results might be. Otherwise you could have large uncertainties that you
> >cannot estimate. I expect that most journal reviewers would want them
> >included. Independent runs from different seeds are good, and in my
> opinion
> >runs from different initial structures can be better. Keep in mind that
> the
> >errors bars are a lower bound on the true uncertainty.
> >
> >On Mon, Jan 13, 2020, 10:36 AM Qing Lv <lvqingjiejie.163.com> wrote:
> >
> >> Dear All,
> >>
> >>
> >> I wonder if the error bars are necessary for umbrella sampling in PMF
> >> calculation? If yes, how should the error bars be calculated? Need I do
> 2~3
> >> repeats (with different random initial velocities assigned)?
> >>
> >>
> >> Thanks,
> >> Qing
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Received on Tue Jan 14 2020 - 04:00:02 PST
