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

[Oliver Beckstein]

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
experience.

Oliver


> Another measure would be to check the distribution of ions around the
> protein.
> >
> > TIA
> >
> > Cheers,
> > Alan Wilter
> > Brazil
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
>

--
Oliver Beckstein * oliver at biop.ox.ac.uk
 http://sansom.biop.ox.ac.uk/oliver/