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

[Justin Lemkul]

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.

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

-- 
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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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