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

Andre Farias de Moura andre at qt.dq.ufscar.br
Mon Aug 2 13:00:14 CEST 2004

dear all,

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?

best regards,



    Dr. Andre' Farias de Moura


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


        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


More information about the gromacs.org_gmx-users mailing list