[gmx-users] PME

Ran Friedman ran at hemi.tau.ac.il
Tue Mar 16 17:16:00 CET 2004

Did you try using PME with a net charge in Gromacs?

As far as I know, the unit cell should be neutral according to Darden et
al. This was mentioned also by Ibragimova and Wade  and by Bogusz et al.
in the context of macromolecular simulations (Biophys. J. 74:2906; J.
Phys. Chem. 108: 7070). As discussed in the latter reference, the
implicit neutralisation can lead to artefacts.


Michael Brunsteiner wrote:

> --- 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 Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university

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