[gmx-users] charmm36 ions fix

[Justin Lemkul]

On 6/21/16 6:29 AM, gromacs query wrote:
> Hi Justin
>
>>> Follow the analysis of the Venable paper
>
> I think you mean this paper: http://pubs.acs.org/doi/abs/10.1021/jp401512z
>

Yes, exactly.  Because you need to determine if what you are seeing is real or 
artificial.  What they did in that paper was figure out that the results without 
the NBFIX are artificial because there are known experimental data for those 
systems.  Subsequent analysis of distributions of ions, etc showed the source of 
the problem and hence the need for the NBFIX.  If you're seeing lipid ordering 
with increased salt, that is expected; what you need to determine is if it's 
incorrect or not.  I suspect it's probably fine, given the range of 
concentrations for the osmotic pressure calculations, but never say never when 
dealing with force fields and systems that haven't been explicitly addressed yet.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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