[gmx-users] Lennrd-Jones potential in Gromos force field

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 14 08:54:32 CEST 2018


No. The effects are not separable, and you are anyway ignoring entropic
effects. You can measure a free energy of binding for each drug with each
CNT functional group and have a reliable way to rank things.


On Thu, Jun 14, 2018 at 8:45 AM <kordzadeh at aut.ac.ir> wrote:

> ​Thank you Dr.Abraham for your answer
> I used different functional groups for functionalization CNT, I determined
> polarity with dipole moment that can be calculated using partial charges by
> VMD,
> my goal from these question is to find a way to separate type of
> interaction between drug and functionalized CNT (polar-polar or
> nonpolar-nonpolar)and show how polar-polar interaction differ for different
> functional group, now I calculated LJ-SR between f-CNT and drug, Do you
> think if I define functional group as a ''energy grp" I can calculate only
> interaction of polar groups?
> Thanks in advance for your help
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