[gmx-users] Implicit solvation: nonpolar term?

[Justin Lemkul]

On 12/19/13 6:14 PM, rdwducl wrote:
> Thanks for the reply Justin but I'm confused. Why must the atoms be bonded?
>
> Ultimately I plan to model micellisation whereby surfactants, which only
> interact with each other via non-bonded terms, are driven to aggregate by
> this nonpolar term...
>

I'm making a somewhat educated guess based on what you're observing.  A 
trivially simple test is to run two calculations with two particles in a box - 
one in which a bond is defined between them, and one in which there is no bond, 
but the atoms are at the same distance.  If the results are different, my 
suspicion is confirmed (that the topology controls whether or not two atoms 
impact one another's surface accessibility).

Give that a try and see what happens.

-Justin

-- 
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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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