[gmx-users] Fwd: Implicit solvent simulation

prasun kumar prasun30 at gmail.com
Mon Feb 10 17:31:48 CET 2014

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

Thanx alot in the advance

Desire + stability = Resolution
Resolution + Hard work = Success

On Mon, Feb 10, 2014 at 8:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 2/10/14, 7:47 AM, prasun kumar wrote:
>> Dear All
>> I am planning to study the effect of adding the ions on the dodecamer
>> protein.
>> For this purpose I need to add ions (Fe2+) in the system. Any suggestion
>> for it. I have come to know through  various discussion forums that  there
>> is no need of adding ions to make the system neutral, but in my case I
>> have
>> to add ions, how will be mdp file look for ions added system.
> You wouldn't use genion in this case.  In the case of implicit solvent,
> there's nothing to delete to replace with the ions.  genbox -ci -nmol is
> what you want here, though it is questionable whether this sort of
> representation is at all meaningful.  Hydrated ions (especially transition
> metals) have very complex properties.  I'd suspect in an implicit solvent
> system, a lot of the behavior will not represent reality.
> -Justin
> --
> ==================================================
> 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
> http://mackerell.umaryland.edu/~jalemkul
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