How to extract potential energy after simulation?

User discussions
1

I got zero in the file size of PE.xvg which is the output of potential energy as I used this command
gmx energy -f tprout.edr -s tprout.tpr -o PE.xvg that show

Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
  1  Angle            2  Proper-Dih.      3  Improper-Dih.    4  LJ-14         
  5  Coulomb-14       6  LJ-(SR)          7  Disper.-corr.    8  Coulomb-(SR)  
  9  Coul.-recip.    10  Potential       11  Kinetic-En.     12  Total-Energy  
 13  Conserved-En.   14  Temperature     15  Pres.-DC        16  Pressure      
 17  Constr.-rmsd    18  Vir-XX          19  Vir-XY          20  Vir-XZ        
 21  Vir-YX          22  Vir-YY          23  Vir-YZ          24  Vir-ZX        
 25  Vir-ZY          26  Vir-ZZ          27  Pres-XX         28  Pres-XY       
 29  Pres-XZ         30  Pres-YX         31  Pres-YY         32  Pres-YZ       
 33  Pres-ZX         34  Pres-ZY         35  Pres-ZZ         36  #Surf*SurfTen 
 37  T-Protein                           38  T-non-Protein                     
 39  Lamb-Protein                        40  Lamb-non-Protein                  

10

Last energy frame read 200000 time 200000.000         

Statistics over 100000001 steps [ 0.0000 through 200000.0000 ps ], 1 data sets
All statistics are over 1000001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Potential                  -87747.3        4.1    290.237   -25.9832  (kJ/mol)

GROMACS reminds you: "People are DNA's way of making more DNA." (Edward O. Wilson)
2

The output looks completely OK from the GROMACS side. I would suspect that for some reason the PE.xvg output file cannot be written. Is the file already existing and read-only?

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3

yes thanks a lot, i checked it again and worked, Thanks a lot but is there any relation between energy groups and potential energy as i didn’t run or use energy groups in equilibration or simulations phase

4

Interaction energy is an optional quantity that one can calculate as a post-processing task if it is needed. It does not have any impact on whether or not the system’s potential energy is computed.

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