[gmx-users] using enegygrps
jalemkul at vt.edu
Wed Feb 14 19:29:18 CET 2018
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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