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

[Mark Abraham]

Good points, Alex!

Mark

On Thu, Jun 14, 2018 at 9:15 AM Alex <nedomacho at gmail.com> wrote:

> 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 <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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