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
charges.
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 ..
Best
Ivan
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
