[gmx-users] zero value for non-Protein components in energygrps

[Mohammad Hassan Khatami]

Hi,

I have an issue with calculating energy groups in GMX2016.4, while 
running a simple protein in water tutorial using the default oplsAA 
forcefield in gromacs. I searched my problem it in the mailing list but 
did not find my answer.

In addition to the default tutorial results, I wanted to print out the 
energy values for different components of the simulation, i.e., protein 
and water, in the .edr file. So I added the line below to the .mdp file 
to calculate values for different energy groups:


energygrps = Protein SOL

After running a short simulation, I calculated the different energy 
values and the output is as follow:

Energy                      Average   Err.Est.       RMSD Tot-Drift
-------------------------------------------------------------------------------
LJ-14                           3004.95        5.3     54.675 44.9933  
(kJ/mol)
Coulomb-14                 7927.05        4.1    44.0138 -4.19923  (kJ/mol)
LJ (SR)                         21978.8        110    500.505 752.675  
(kJ/mol)
Coulomb (SR)               -208384        220    1438.51 -1321.11  (kJ/mol)
Coul-SR:Protein-Protein -208384        220    1438.51   -1321.11 (kJ/mol)
LJ-SR:Protein-Protein      21978.8        110    500.505 752.675  (kJ/mol)
Coul-14:Protein-Protein   7927.05        4.1    44.0138 -4.19923  (kJ/mol)
LJ-14:Protein-Protein       3004.95        5.3     54.675 44.9933  (kJ/mol)
Coul-SR:Protein-SOL               0          0          0 
0                (kJ/mol)
LJ-SR:Protein-SOL                   0          0 0          0            
     (kJ/mol)
Coul-14:Protein-SOL               0          0          0 0              
    (kJ/mol)
LJ-14:Protein-SOL                   0          0 0          0            
      (kJ/mol)
Coul-SR:SOL-SOL                    0          0 0          0          
        (kJ/mol)
LJ-SR:SOL-SOL                        0          0 0          0          
        (kJ/mol)
Coul-14:SOL-SOL                    0          0 0          0          
        (kJ/mol)
LJ-14:SOL-SOL                        0          0 0          
0                 (kJ/mol)

Here, all the energy values for the Protein-SOL and SOL-SOL are zero, 
which is not what I expected. Moreover, the general LJ-14, Coulomb-14, 
LJ (SR) and Coulomb (SR) are exactly the values calculated for only protein.

When I run them individually, i.e., only water system and only protein 
system, I get non-zero values, which are expected.

Is there any other flag except  "energygrps" that I forgot to implement 
in my mdp file? and why is it only calculating the values of the 
protein  in the general LJ-14, Coulomb-14, LJ (SR) and Coulomb (SR) 
energies.

Best,

MHK