[gmx-users] using enegygrps

[Justin Lemkul]

On 2/14/18 1:15 PM, kordzadeh at aut.ac.ir wrote:
> Hi all
>
> I want to investigate interaction drug and bilayer for more detailed investigation I want to use energygrps for functional group of drug to find out which part of drug has more interaction.
>
> is energygrps good tool?

If the force field you're using was parametrized in such a way that the 
nonbonded energy decomposition has some physical meaning, maybe. But 
chopping a molecule into pieces and calculating pairwise nonbonded 
energies is not a useful approach. An entire molecule, for the purpose 
of comparison, maybe.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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