[gmx-users] Query regarding energy calculation

[Justin Lemkul]

On 2/19/16 3:09 PM, Tushar Ranjan Moharana wrote:
> Hi everyone,
> I want to calculate energy (non-bonded) between various amino acids. I have
> the following queries:-
>
> 1)   If an atom belongs to two different energy groups it is showing error.
> Is there any way other than using mdrun -rerun. It is fine for me if energy
> between those groups which share atom/atoms will not be calculated.

If you want different groups that include overlapping sets of atoms, you need to 
do those calculations in separate instances of mdrun -rerun.

> 2)   If a protein is simulated at two local minima (let us say lid open and
> closed form of lipase) and energy is extracted (total or potential) can I
> say the difference in energy is delta G. If not then what is the
> significance of potential and total energy extracted by gmx energy
> (g_energy).
>

It's not delta G.  The energies are what they say they are - potential and total 
energy.  The interaction energies are force field-dependent estimations of 
enthalpic contributions to the potential energy.  Whether or not the force field 
you're using can produce meaningful values is another question.  But it's 
certainly not delta G.

-Justin

-- 
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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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