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

[Justin Lemkul]

On 10/31/17 12:07 PM, Mohammad Hassan Khatami wrote:
> 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.
>

If you did the simulation on GPU, energygrps are not supported. Do an 
mdrun -rerun on the trajectory using just CPU hardware to obtain these 
energies.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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