[gmx-users] Re: What is 'rest' in g_energy

[Markus O Kaukonen]

>> I define in .mdp file:
>> >energygrps               = HER HEA r_239
>> >energy_grp_excl          = HER HER HEA HEA r_239 r_239
>> The after md one runs g_energy.
>> Question: What is the group 'rest' in the g_energy input?

>you define three groups for energy, rest is everything else. (Spoel)

Hi again,
Then I'm puzzled because g_energy output gives

>Energy                      Average       RMSD     Fluct.      Drift
>-------------------------------------------------------------------------------
>Coulomb (LR)                -286562    2759.25          0   -688.375
>Coul-LR:HER-HER                   0          0          0          0
>Coul-LR:HER-HEA                   0          0          0          0
>Coul-LR:HER-rest                  0          0          0          0
>Coul-LR:HEA-HEA                   0          0          0          0
>Coul-LR:HEA-rest                  0          0          0          0
>Coul-LR:rest-rest                 0          0          0          0

Why there is no long range coulomb interaction?
I use PME with parameters
   rlist                = 0.9
   coulombtype          = PME
   rcoulomb_switch      = 0
   rcoulomb             = 0.9

Is all coulomb interaction (except with background charge) within the
system defined as 'short range' with this setup?

System is a protein in a water box with dimension about 10nm x 10nm x 10nm

Terveisin Markus

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