Re: [AMBER] Is error bar necessary for umbrella sampling?

From: Qing Lv <>
Date: Tue, 14 Jan 2020 10:48:06 +0800 (CST)

Thank you so much. Are there any tools in Amber or elsewhere to make such error bars from umbrella sampling?


At 2020-01-13 22:42:49, "Carlos Simmerling" <> 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 <> 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 Mon Jan 13 2020 - 19:00:02 PST
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