[gmx-users] Regarding the Pi-Pi and pi-cation interaction

[Ivan Gladich]

Hi,
to the best of my knowledge,
Molecular Dynamics is not the best way to study system stabilized by 
Pi-Pi or Pi-Cataion interaction.

However,in MD  people usually overpolarized C-C and C-H bonds to
increase the quadrupole interactions, and thus, mimic the Pi-Pi 
interaction

See
http://pubs.acs.org/doi/pdf/10.1021/jp408977b
or
http://pubs.rsc.org/en/content/articlelanding/2006/cp/b610253k#!divAbstract

In conclusion (and in my opinion), you case use MD but be careful and 
test your Force field...

Ivan

On 2014-10-30 05:55, rama david wrote:
> Dear Friends,
> 
>  I search the archive to find the answer of my question but I did not 
> get
> satisfied answer so I am putting the question in forum.
> 
> One of them is as
> http://comments.gmane.org/gmane.science.biology.gromacs.user/51771
> 
> I want to study the MD simulation of Ligand and Receptor that is 
> stabilize
> by
>  Pi-Pi and pi-cation interaction
> 
> 1.  Is it right to say the  Pi-Pi and pi-cation interaction can be 
> studied
> by Molecular    dynamics??
> 
> 2.  Which force field I have to use ??
> 
> 3. In the analysis tools I found that no direct tools can do this 
> directly.
>     How to do this analysis
> 
> I am looking forward for reply.
> 
> With best regards,