[gmx-users] combining energy files

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> I am using gromacs-4.0.5.

Try upgrading to the newest version (4.0.7), and if that does not fix the 
problem, please report back with the exact command line, gmxcheck output (on the 
.edr file), compilers used, hardware, etc.

-Justin

> 
> 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
>>>
>>>
>>> -- 
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before 
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use thewww
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================