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

Ivan Gladich igladich at sissa.it
Thu Oct 30 14:51:09 CET 2014

On 2014-10-30 13:10, Justin Lemkul wrote:
> On 10/30/14 4:57 AM, Ivan Gladich wrote:
>> 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...
> Wouldn't this increase in polarization along these bonds require
> reparametrization of bonded interactions, as well?  Everything is
> interrelated.  Even if you get the quadrupole moment better, I would
> think there are potential issues with the bonded parameters.  I guess
> your relative energies show that the approach is OK, but I would
> imagine doing this in some force fields would have big implications
> for the integrity of the model.

I perfectly agree with you..
Indeed, we increased the polarization with a small scaling up of the 
As you said, scaling  too much you get in troubles.

Scaling the charges helps the force field but it does not solve
the problem. For example, even with this trick, you cannot get a perfect 
pi-stacking in MD
,as shown in the first paper for Naphthalene, but you get a parallel 
displaced dimer (Figure 6D).
As I said, MD is not the best way to study these kind of systems...
depends on what you need and the accuracy that you want ..

> Apologies if any more details described in the second article; our
> university does not have access to that journal so I am only reading
> the JPCA article.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> ==================================================

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