[gmx-users] combining energy files

[nishap.patel at utoronto.ca]

I am using gromacs-4.0.5.

Thanks.



Quoting XAvier Periole <x.periole at rug.nl>:

> 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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