[gmx-users] Total energy -decomposed terms

Moeed lecielll at googlemail.com
Mon May 17 17:23:22 CEST 2010

Dear Justin,

Thanks so much for your comments. As for my question below:

... Also, do LJ energy figures (or
coulomb) given by g_energy refer to e11,e22.. interaction energies?

Justin: By default, you will not get these interaction energies decomposed
as you would
like.  You can, however, set "energygrps" in the .mdp file to separate out
contributions.  If using PME, however, there will be a long-range term that
simply cannot be decomposed, so choose your long-range electrostatics method

I go ahead and read about energy groups but I have a question here. So what
are the energy terms like LJ or coulomb one gets from g_energy. Are they not
the decomposed terms from total energy of system? Can I not take for
instance LJ energy values which are coming from a specific NO. of molecuels
in simulation box and calculate interaction energies for pairs or "mol"
number of molecules?

Thank you for you help :)

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