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

Yanmei Song ysong30 at asu.edu
Fri Nov 20 23:39:21 CET 2009

```Dear Justin:

Thank you so much for your quick response.

But I still don't get it. Should I calculate the standard error manually by
using the equations A17 (in B. Hess' s paper) after I get the result by
g_analyze. And then which value I should use for the sigma?

Here is the output :

invalid fit:  e.e. 15.6513  a 2.17585  tau1 28.9321  tau2 46.3966
Will use a single exponential fit for set 1
Set   1:  err.est. 21.0339  a 1  tau1 15.1648  tau2 0

I really appreciate your patience and help!

On Fri, Nov 20, 2009 at 3:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Yanmei Song wrote:
>
>> 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
>>
>>
> The relationship is not a simple inversion as you've shown it.  That is,
> (standard error of 1/eta) != 1/(standard error of eta).  The standard error
> calculation depends on a number of factors, hence all the math in the
> Appendix :)  An example is given in Fig. 8 of that paper.
>
> -Justin
>
>
> --
> ========================================
>
> 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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