[gmx-users] Energy Decomposition

[Justin Lemkul]

On 3/6/15 9:24 AM, xy21hb wrote:
> Dear Gmxers,
>
>
> I have a binary system, e.g. protein in water. I would like to have the energy of the water over the trajectory.
>
>
> I can do
> 1.
> using "energygrps = Protein SOL", it only gives, LJ-14, Coul-SR, .... energies, but the Energy still shows for the whole system
>

Because that's what energygrps is used for, a decomposition of short-range 
nonbonded energies.  It will not decompose bonded terms, PME mesh, etc.

>
> 2.
> using index.ndx to trjconv the total traj into SOL only traj and then g_energy
>

Coupled with a new .tpr file that matches, and subsequently mdrun -rerun, this 
might give you what you're after, but the "energy of water" or "energy of the 
protein" seem like fairly arbitrary numbers to me.  Interaction energies can be 
valuable, if the force field was parametrized with such a quantity in mind.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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