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

David spoel at xray.bmc.uu.se
Mon Jan 13 19:50:04 CET 2003

On Mon, 2003-01-13 at 20:39, David L. Bostick wrote:
> All in all however... it depends on what you want to look at..  If you are
> interested in things that are rather relatively insensitive to the large
> scale polarization of solvent (i.e. protein shape etc.) then it may be
> perfectly fine to use tinfoil boundary conditions.
> Yes ... it only affects the surface term, but the essence of the
> conditional convergence of the Ewald sum is encapsulated in this term.  If
> you take a spherical sum you get one answer.  If you take a slab-wise sum
> you get another.  We are dealing with the behavior of the system at
> infinity, then again, with periodic boundaries, we are simulating an
> infinite system.  .. Seems philosophical, but it can make a difference.
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 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?

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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