[gmx-users] charge in bilayers

[David L. Bostick]

I imagine you are using PME for electrostatics.  This should be okay as
long as the charge is small.  1 Na+ should be fine.  The ewald method gives
a background charge to counter the +1 charged ion. This introduces
systematic error to the calculation.  The smaller the charge, the smaller
the error. Also, the bigger the system, the smaller the error. A decent
sized bilayer system ~100 lipids or more with water should be enough to
counter the effects.

For discussions on this matter, see papers of e.g. Hunenberger or G.
Hummer.

David

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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On Thu, 27 Oct 2005, Rama Gullapalli wrote:

> Dear GMX ers
> This is quite a basic question. If i wanted to
> simulate the presence of a Na+ ion in a electrically
> neutral bilayer such as DPPC,
> Is it a problem to run this simulation in GMX without
> adding the counterion?
> I mean GROMPP gives a warning saying there is 1 charge
> in the system.
> Does it affect the simulation in any way?
> Thanks
> Regards
> Rama
>
>
>
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