[gmx-users] combining energy files

[XAvier Periole]

That looks like a nice bug!

You should specify which gmx version you are using. That would help  
getting it fixed.

On Apr 13, 2010, at 21:34, nishap.patel at utoronto.ca wrote:

> Hello,
>
>   I am a running a simulation of 100ns, so I have two edr files  
> md.edr and md.part0002.edr. When I calculate some of the energy  
> values using g_energy for each of the .edr files individually I get  
> the following result:
> For md.edr:
> Statistics over 27120401 steps [ 0.0000 thru 54240.8008 ps ], 4 data  
> sets
> All averages are over 271205 frames
>
> Energy                      Average       RMSD     Fluct.       
> Drift  Tot-Drift
> --- 
> --- 
> --- 
> ----------------------------------------------------------------------
> Temperature                 297.996    3.75973    3.75972  
> 6.88223e-07  0.0373298
> Pressure (bar)              1.66199    262.287    262.287  
> -2.24459e-05   -1.21748
> Volume                      66.1617    0.39728    0.39728           
> 0          0
> Density (SI)                983.924    5.90292    5.90292  
> -1.44217e-07 -0.00782243
> Heat Capacity Cv:      12.4747 J/mol K (factor = 0.000159181)
> Isothermal Compressibility: 5.79816e-05 /bar
> Adiabatic bulk modulus:        17246.9  bar
>
> For md.part0002.edr
> Statistics over 22986601 steps [ 54026.8008 thru 100000.0078 ps ], 4  
> data sets
> All averages are over 229867 frames
>
> Energy                      Average       RMSD     Fluct.       
> Drift  Tot-Drift
> --- 
> --- 
> --- 
> ----------------------------------------------------------------------
> Temperature                 297.993    3.75398    3.75397  
> -5.66217e-07 -0.0260308
> Pressure (bar)              1.51511    263.692    263.692  
> 4.88234e-05    2.24457
> Volume                      66.1617   0.398494    0.39849  
> 1.29794e-07 0.00596703
> Density (SI)                983.924     5.9329    5.93284  
> -1.92684e-06  -0.088583
> Heat Capacity Cv:      12.4747 J/mol K (factor = 0.000158697)
> Isothermal Compressibility: 5.8337e-05 /bar
> Adiabatic bulk modulus:        17141.8  bar
>
> But then when I combined my .edr files using eneconv -f md.edr  
> md.part002.edr. the output is saved into 'fixed.edr' and when I ran  
> fixed.edr file through g_energy, I get negative values as follows :
> Statistics over 50000001 steps [ 0.0000 thru 100000.0078 ps ], 4  
> data sets
> All averages are exact over 50000001 steps
>
> Energy                      Average       RMSD     Fluct.       
> Drift  Tot-Drift
> --- 
> --- 
> --- 
> ----------------------------------------------------------------------
> Temperature              -5.90251e-06          0          0           
> 0          0
> Pressure (bar)           4.46175e-06          0          0  
> -9.66961e-07 -0.0966961
> Volume                   -1.32585e-06          0          0           
> 0          0
> Density (SI)             -1.96389e-05          0          0  
> -2.119e-07   -0.02119
> Heat Capacity Cv:      12.4718 J/mol K (factor = 0)
> Isothermal Compressibility:          0 /bar
> Adiabatic bulk modulus:            inf  bar
>
> I don't understand what happened there. Could someone please help me  
> understand if I am combining the files correctly, or it is something  
> I am missing.
>
> Thanks
>
> Nisha Patel
>
>
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