[gmx-users] reference distance for Lennard Jones interactions

[Justin Lemkul]

On 10/18/18 8:34 AM, kordzadeh at aut.ac.ir wrote:
> ​Hi
> I have calculated Lennard Jones interaction between drug and Carbon Nano tube by defining "energygroups" and I got the potential by "gmx energy"
> I have a question, in this figure I have potential versus distance (r), what is the distance? in Lennard Jones equation the distance defines between two atoms, but I don't know what distance will Gromacs consider for interaction while the drug and CNT have a lot of atoms

gmx energy does not write energies as a function of distance, it writes 
energies as a function of time. The interaction distances (e.g. whatever 
is considered short-range) is set by the cutoffs used in the simulation.

-Justin

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

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