[gmx-users] Re: Limitations of simulations?

[Justin Lemkul]

On 7/25/13 12:44 AM, Jonathan Saboury wrote:
> Hm, I am probably completely wrong about this, but can you do implicit
> solvent and Periodic Box Conditions?
>

That's not typical.  I suppose one could do an NVT simulation, but the only 
stable way I have found to run in implicit solvent is to use infinite cutoffs, 
which precludes the use of PBC.  Even "long" cutoffs typically do not produce 
reasonable energy conservation, at least in my hands.  Then there's the matter 
of unscreened long-range interactions.

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

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