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

[Andre Farias de Moura]

dear berk,

I have not made myself clear: I know the way averages are calculated,
but concatenated files give almost a 10-fold difference in average!
please look more carefully at the average values I reported in my
previous message, the differences are too large to be just a matter
of precision!

thanks again,

andre'

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

    Dr. Andre' Farias de Moura

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

  Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
     Sao Carlos - SP - Brasil

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        Endereco Atual

    Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
    Universidade de Sao Paulo
    Sao Carlos - SP - Brasil
    Telefone: 55-16-3373-8055

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On Mon, 2 Aug 2004, Berk Hess wrote:

> 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
> accurate.
>
> 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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