[gmx-users] g_energy averages

Erik Lindahl lindahl at stanford.edu
Wed Jul 17 19:03:41 CEST 2002

David L. Bostick wrote:
> HI,
> I use g_energy on an edr file from a constant surface tension simulation.
> I printed out Box-X, Box-Y, and Box-Z lengths and Press-XX, Press-YY, and
> Press-ZZ pressures.  I am trying to fine tune a bilayer/protein system in
> order to preserve the xy-area of the box.  I parsed the xvg file using a
> simple awk script in order to calculate area, surface tension, average
> pressures.. etc, but when comparing the values to those generated by
> g_energy, there is a small discrepancy.  I am pretty sure I am calculating
> things  correctly.  Does g_energy use some other precision for it's
> calculation of averages and so forth?

Well, not a different precison but a completely different algorithm :-) 
It is described in detail at the end of the manual.

We actually store a couple of partial sums in the energy file, which 
makes it possible to calculate the REAL average and fluctuation from all
the simulation steps - not only the average of the values written to the 
energy file.

It's kind of complicated; the easiest way to do it (as you've probably 
seen in a statistics textbook) is to store the sum and sum-of-squared
values, but that leads to numerical inaccuracies for longs trajectories,
thus the need for partial sums.



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