[gmx-users] How to calculate the block averaging error from non-equilibrium MD simulations

[Yanmei Song]

Dear Justin:

I really appreciate your response and help!

I am confusing about the result by using this method. I found in B. Hess's
paper (Appendix, JCP, 116, 2002)  that " this gives a standard error
estimate for 1/eta of 29.5. "; and the error he gives for that eta is 0.006.
I thought the error should be calculated as 1/29.5=0.034. Thank you again
for your help!

On Fri, Nov 20, 2009 at 12:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Yanmei Song wrote:
>
>> Dear Users:
>>
>> Anyone knows how to get the standard errors of the results based on block
>> averaging from non-equilibrium MD simulations? I am trying to get the error
>> estimations for my calculated viscosity of the fluid. Any command can give
>> me that? or I have to do it manually? Thank you in advance!
>>
>
> From g_analyze -h:
>
> "Option -ee produces error estimates using block averaging. A set is
> divided
> in a number of blocks and averages are calculated for each block. The error
> for the total average is calculated from the variance between averages of
> the
> m blocks B_i as follows..."
>
> -Justin
>
>
>
>> --
>> Yanmei Song
>> Ph.D. Candidate
>> Department of Chemical Engineering
>> Arizona State University
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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