[gmx-users] Fwd: Implicit solvent simulation

[prasun kumar]

Dear Justin

Sending you the personal email for thanking you for the quick reply and the
tutorials you have put on your website (especially Umbrella sampling)
Thanx alot.


PRASUN (ASHOKA)
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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