[gmx-users] Help about 2 D periodic boundary condition

[David L. Bostick]

> Thanks for your comments. OK, let me be a bit more specific: I would
> like to compute surface tensions of liquid mixtures. I do not know what
> epsilon_surface to use. I could of course use the bulk value of the
> dielectric constant that I compute from a bulk simulation. Is that
> correct? (I'm pretty sure I can get away with it but ... )
>
I think traditionally, infinity is used for that (whether it's the correct
thing to do is another story).  However, I agree with your "but ..." - it
seems fishy to simulate bulk water for a dielectric constant and plug it
into another simulation because, after all, what dielectric constant does
one use to begin with?

> I have also played a bit with epsilon_surface in water simulations. If
> you use the value you put in for epsilon_surface for computation of the
> dielectric constant (g_dipoles -epsilonRF epsilon_surface) you get the
> same dielectric constant in all cases. However the Debye relaxation time
> (which happens to be roughly correct fo SPC/E with tin-foil BC) is
> ruined by using epsilon_surface not infinity. This makes me a bit
> suspicious... Or is there a correction for this too?

Ok, that's difficult.  I don't believe I can answer that, but again, when
you set epsilon_surface, it is for r->infinity from the central simulation
cell.  It is difficult to say how different dielectric constants affect
things.  The JCP I cited in the previous message about dielectric constant
calculation used a 2D sum.  They simulated a slab of water between 2
Pt(111) surfaces with and without an applied electric field and calculated
the dielectric constant directly.  When calculating the dielectric constant
with 3D boundary conditions the result is well known to be dependent on the
boundary conditions adopted. With 3D geometry, water can behave very
strangely in a large electric field due to the images around the central
image.

I know this doesn't answer your question completely, but I hope it helps
David

>
>
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 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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