[gmx-users] What's the point of adding ions to neutralize the system?

Justin Lemkul jalemkul at vt.edu
Thu Aug 20 22:44:34 CEST 2015

On 8/20/15 4:15 PM, Victor Rosas Garcia wrote:
> You said it yourself: to neutralize the net charge of the system.

Great answer: "you neutralize the system in order to neutralize the system" :)

>> Since the ion added is usually very far away from the protein (or molecule
>> of interest), I don't see how it can affect the results of the molecular
>> dynamics simulation. So why is it so important to add ions to neutralize
>> the net-charge of the system?

One effect is practical - in the absence of a net-neutral system, PME applies a 
neutralizing background charge, which for a homogeneous medium, is an adequate 
approximation.  But this is a very bad approximation in many other cases.  There 
are even relevant inhomogeneities at protein surfaces, though the effects are 
not as profound as, say, in a membrane system.

Second point - life exists in salt.  We like to model things that are 
biologically relevant.

Third and final point - it is fundamentally incorrect to assume that there will 
be no effect of the ions.  DNA dynamics are exquisitely sensitive to ionic 
concentration, for instance (though additive models are not nearly as responsive 
as polarizable ones, there are some effects).  Protein salt bridges are affected 
by ionic concentration, even if the interactions are not direct, there is a 
change in ionic environment within a hydration shell or two and that will affect 
dynamics.  And even if ions are far away from the solute to start, they don't 
stay there...


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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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