[gmx-users] reference distance for Lennard Jones interactions

Justin Lemkul jalemkul at vt.edu
Sat Oct 20 00:33:40 CEST 2018

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 A. Lemkul, Ph.D.
Assistant Professor
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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