[gmx-users] Fwd: Implicit solvent simulation
prasun30 at gmail.com
Mon Feb 10 17:28:22 CET 2014
Sending you the personal email for thanking you for the quick reply and the
tutorials you have put on your website (especially Umbrella sampling)
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
>> 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
>> 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 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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