[gmx-users] g_energy averages don't match xmgrace values

Berk Hess gmx3 at hotmail.com
Mon Aug 2 15:47:39 CEST 2004

The averge and rmsd are accumulated in the energy file
using all MD steps, not just the ones stored in the energy file.
The g_energy Average and RMSD output are therefore more

Please read the manuals:
g_energy -h
and the pdf manual.

>I'm using g_energy to calculate the surface tension of organic
>films on water but g_energy output (average, rmsd, etc) don't
>match the values I get using xmgrace to analyze the energy.edr
>file taht is generated.
>g_energy gives the output:
>Energy        Average RMSD    Fluct. Drift     Tot-Drift
>#Surf*SurfTen 9.31348 1546.39 1544.9 -0.517532 -235.141
>while grace gives:
>mean : 81.2055
>stdev: 4207.49
>if I perform a linear regression using grace the slope I get is
>exactly the same as the drift above: -0.51753.
>the file energy.edr was generated by eneconv -f out*.edr -settime.
>I've set 'c' flag for the first edr file (t=0 ps) and 'l' flag for
>the remaining ones. I've done the same calculations on other data
>and the difference between g_energy and grace was also found.
>if I use only one of these out*.edr files, e.g. out06.edr, a better
>agreement may be found:
>g_energy outputs:
>Energy        Average RMSD    Fluct.  Drift    Tot-Drift
>#Surf*SurfTen 115.168 4242.39 4242.13 -1.63609 -163.611
>while grace outputs:
>mean : 133.849
>stdev: 4183.75
>even in this case, there isn't a quantitative agreement and I'm
>wondering why: is it a bug or am I doing something wrong?

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