[gmx-users] monitor energy

[Gerrit Groenhof]

Hi Rui,

>        I am trying to compute the interaction energy between groups in my
> simulation. I am not clear on how the interaction energy is computed. The
> short range interaction is not a problem, but how to compute the
> long-ranged electrostatic interaction energy? For example, if one want to
> compute the electrostatic interaction between one ion with another group,
> how should one proceed?

You can use the energygroups option in the mdp file. Just put the ions
you are interested in seperate energygroups. The interaction energy of
each energy group with the others is monitored and stored to the
ener.edr file. So just analyse the energy file with g_energy
afterwards.

>        In addition, Gromacs is reporting LJ interaction, Coul-SR and
>Coul-LR for the energies. Since I am using PME, it is confusing to me why
> the Coul-SR is still reported.

hmmm, i guess, but am not sure, that this SR is the lattice sum in
real space

good luck,

Gerrit