[gmx-users] PME, netcharge, implementation, counterions
oliver at biop.ox.ac.uk
Fri May 14 13:37:05 CEST 2004
On Fri, 14 May 2004, David van der Spoel wrote:
> 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....
For 4x4x4 boxes of 1M NaCl at std conditions it takes about 15-20 ns to
reach relatively homogeneous densities, and similar times (~10 ns) seem
to apply in simulations of membrane embedded proteins, at least in my
> Another measure would be to check the distribution of ions around the
> > TIA
> > 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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Oliver Beckstein * oliver at biop.ox.ac.uk
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