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

Alex nedomacho at gmail.com
Thu Jun 14 09:15:21 CEST 2018

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.


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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