[gmx-users] reference distance for Lennard Jones interactions

[kordzadeh at aut.ac.ir]

​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
Please help me for this problem
Thanks in advance
Best Regards
Azadeh

-- 
This email was Anti Virus checked by  Security Gateway.