[gmx-users] charmm36 ions fix

[gromacs query]

Thanks Justin, your inputs are really helpful. I did basic analysis on
thickness which increased slightly with salt conc. (with NBFix) but I do
need to see other things more carefully.

JIomm

On Tue, Jun 21, 2016 at 12:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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