[gmx-users] reference distance for Lennard Jones interactions

Mark Abraham mark.j.abraham at gmail.com
Sat Oct 20 14:04:57 CEST 2018


You have two groups of atoms. The inter-group energy is the sum of all
pairwise interactions between members of each group. It was typically not
parameterized to be meaningful on its own.


On Sat, Oct 20, 2018, 12:27 <kordzadeh at aut.ac.ir> wrote:

> 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
> Regards
> Azadeh
> On Thu, 10/18/2018 05:34 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
> Please help me for this problem
> Thanks in advance
> Best Regards
> Azadeh
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