[gmx-users] reference distance for Lennard Jones interactions

kordzadeh at aut.ac.ir kordzadeh at aut.ac.ir
Sat Oct 20 12:27:11 CEST 2018

Dear Dr.Lemkul​
Thank you for your answer
I get it the cut off radius is distance, when we calculate Lennard Jones (short range) between drug and CNT, what atoms does Gromacs consider for interaction, I mean lennard Jones potential is calculated between two atoms of drug and CNT and then Gromacs will report average of it, I can't understand it drug and CNT have a lot of atoms, is the reported Lennard Jones potential between all of them?
Looking forward to hearing from you

On Thu, 10/18/2018 05:34 AM, kordzadeh at aut.ac.ir wrote:
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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