[gmx-users] Total energy -decomposed terms

[Justin A. Lemkul]

Moeed wrote:
> 
> 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 these
> contributions.  If using PME, however, there will be a long-range term that
> simply cannot be decomposed, so choose your long-range electrostatics method
> carefully.
> 
> ****************************************************
> 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 

The default terms are the total LJ and Coulombic energy terms for the system. 
That could include both intra- and intermolecular terms.  If you want the LJ and 
Coulombic energy between molecules A and B, you have to set:

energygrps = A B

in the .mdp file.  Then you will get LJ and Coulombic terms for the interactions 
between these two molecule types, as well as A-A and B-B terms.

> 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?
> 

Not easily.  You will still have intramolecular terms that are not covered by 
the 1-4 interactions.  For example, if the two ends of your molecule interact 
with one another, this interaction will contribute to your nonbonded energies.

You could do your simulation, then use mdrun -rerun with a new topology that 
defines all possible intramolecular exclusions in order to save only 
intermolecular energy contributions.  Doing a simulation like this would be 
meaningless, of course, but you can rerun the simulation to break down the 
energies (that's usually what mdrun -rerun is used for).

-Justin

> Thank you for you help :)
> 
> Moeed
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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