[gmx-users] reference distance for Lennard Jones interactions

kordzadeh at aut.ac.ir kordzadeh at aut.ac.ir
Thu Oct 18 14:34:24 CEST 2018

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
Please help me for this problem
Thanks in advance
Best Regards

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