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

[David van der Spoel]

On Thu, 2004-11-11 at 13:34 +0200, Markus O Kaukonen wrote:
> >> 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?
It's not computed separately. See earlier mails on the mailing list.
> 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
> 
-- 
David van der Spoel <spoel at xray.bmc.uu.se>