[gmx-users] PME, netcharge, implementation, counterions

David van der Spoel spoel at xray.bmc.uu.se
Fri May 14 13:25:48 CEST 2004

On Fri, 2004-05-14 at 13:21, Alan Wilter Sousa da Silva wrote:
> David van der Spoel wrote:
> > It is quite obvious because one usually only has a few ions. Then it
> > takes long before they sample the entire volume of the box. You could
> > say that the ions have reached equilbrium when the ion density in the
> > whole box is uniform when averaged over the simulation (or in fact the
> > density of all molecules in the box).
> And as far as you concern dear Dr. van der Spoel, how long it could be 
> for a common system of protein in water with a couple of ions (~50000 
> atoms)?  Less than 100 ps?
No idea! But it is quite easy to check by running g_density with, say, 1
nm slabs. Of course the protein should also sample the whole box....
Another measure would be to check the distribution of ions around the
> Cheers,
> Alan Wilter
> Brazil
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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