[gmx-users] PME

[Michael Brunsteiner]

--- Ran Friedman <ran at hemi.tau.ac.il> wrote:
> No. You should neutralise the net charge.

not necessarily ... if you use PME (or any other form
of Ewald summation) the neutralization of any netcharge
present in the system is done IMPLICITELY.
(for a good discussion of this point see the manual
of Keith Refsons moldy program)
The effect of this implicit neutraliztion is exactly
the same as the effect a homogeneous "background" charge density
(of the opposite sign as the net-charge and with the same
magnitude when integrated)
For some specific problems (e.g. calculation of free energy
differences between charged and neutral system) corrections
need to be applied, but generally and for a normal MD at constant
volume the artifacts introduced by adding neutralizing counter
ions are certainly not preferable to those obatained from
the homogeneous background charge.


> Ran.
> 
> sadhna wrote:
> 
> > Hi,
> >    can PME be used for systems with net charge??
> >
> > thanks
> > sadhna
> >
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> --
> ------------------------------------------------------
> Ran Friedman
> Laser laboratory for fast reactions in biology
> Department of biochemistry
> Faculty of life sciences
> Tel-Aviv university
> 972-3-6409824
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