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

[Mark Abraham]

Hi,

Note that the easiest way to do that is gmx mdrun -nb cpu -rerun your.trr.
Your original log file did warn you about the zero energies.

Mark

On Tue, Oct 31, 2017 at 8:11 PM Mohammad Hassan Khatami <mhk302 at mun.ca>
wrote:

> Thanks Justin!
>
> That was the issue.
>
> MHK
>
>
> On 2017-10-31 01:35 PM, Justin Lemkul wrote:
> >
> >
> > 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
> >
>
> --
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