[gmx-users] Fwd: Implicit solvent simulation

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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