[gmx-users] Fwd: Implicit solvent simulation

Justin Lemkul jalemkul at vt.edu
Mon Feb 10 18:47:18 CET 2014

On 2/10/14, 11:31 AM, prasun kumar wrote:
> Dear All and Justin
> Thanx for the quick reply...
> My aim is to find the effect of the ion on the dodecamer (whether on adding ions
> it is stable or not)
> Seeing the system.. I am left with two options (My view): 1) Coarse Grain Method
> or 2. Implicit Solvent Method
> Coarse Grain Method is full of approximation thats why I was hesitant to follow
> this approach...

Well, implicit solvation is full of approximations, too.

> According to you if not the implicit solvent method, then any suggestion you can
> give..

Hard to say.  I think there are some significant limitations of MD in general in 
this case.  As I said before, the representation of a metal ion as a simple 
sphere with charge +2 is a fairly poor approximation.  The MD force fields do 
not reproduce effects like charge transfer or maintain proper coordination 
geometry without complex restraints.  If absolutely nothing else, I think you 
need to use an explicit solvent model.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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