I think this terminology (polar/non-polar) might be bad and it can keep
one from understanding the underlying mechanisms.
Also, to add to what Mark said, the whole "polarity" idea is very
unclear and generally impossible to study with MD when it comes to CNTs
and graphene. One must realize that you are not simulating an actual
CNT. You are simulating a collection of LJ+Coulomb particles arranged in
a CNT-like lattice. That is not a CNT. Depending on size,
functionalization, chirality, defects, etc, CNTs may have mobile
electronic charge throughout, which polarizes in the presence of charged
things surrounding the CNT. This comment is easy to ignore, it is
ignored by many people, and I am pretty sure it will be ignored here,
and yet it is very important to keep in mind that you are not simulating
a CNT when it comes to local polarization. It is a very rough
approximation at best.
Alex
On 6/14/2018 12:54 AM, Mark Abraham wrote:
Hi,
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.
Mark
On Thu, Jun 14, 2018 at 8:45 AM <kordza...@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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