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

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 20 23:07:00 CET 2009

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 for your help!

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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