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

Dr. Vitaly Chaban vvchaban at gmail.com
Fri Oct 31 09:59:15 CET 2014

On Thu, Oct 30, 2014 at 5:55 AM, rama david <ramadavidgroup at gmail.com> 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??

No doubts, they can be studied using pairwise interaction potentials within MD.

> 2.  Which force field I have to use ??

I believe all biological FFs maintain pi-pi through adjusted LJ terms.
The difference, as always, is in accuracy, and accuracy in the case of
simulations is a matter of your luck.

> 3. In the analysis tools I found that no direct tools can do this directly.
>     How to do this analysis

In terms of energetics.

Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН

> I am looking forward for reply.
> With best regards,
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