[gmx-users] about periodic boundary conditions

[David L. Bostick]

Hello,

to simulate with 2D boundary conditions, you can use the slab geometry
option for ewald sums and extend the simulation box roughly 3x in the z
dimension. This can be done in gmx with the

ewald_geometry          = 3dc

option for electrostatics.  You can see the following references for
examples of how to use the method properly:

Bostick, D. and M. L. Berkowitz (2003). The Implementation of Slab Geometry
for Membrane-channel Molecular Dynamics Simulations. Biophys. J. 85(1):
97-107.

or

 I.C. Yeh and M. Berkowitz, Ewald Summation for Systems with Slab Geometry,
J. Chem. Phys. 111, 3155-3162 (1999)


David


-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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On Fri, 29 Oct 2004, Haberl Florian wrote:

> > Hi,
> >
> > I want to simulate a system with periodic boundary conditions only in x
> > and
> > y direction, but not in z direction. Are there any ways to realize that?
>
> > Another question is when I install the Gromacs in an Alpha machine, I
> > input
> > the following commands and got:
> >
> > setenv CPPFLAGS -I/home/yy/fftw/include
> > setenv: not found
> >
> > And I tried to input
> >
> > export CPPFLAGS=-I/home/yy/fftw/include
> > CPPFLAGS=-I/home/yy/fftw/include: is not an identifier
> >
> > Can anyone tell me what I should do?
>
> you need to know what kind of shell you are using on your system.
> setenv is for all csh like shells and the export commands for bash like
> shells.
>
> use "echo $SHELL" in your console and it should show you up, like
>
> echo $SHELL
> /usr/bin/tcsh
>
> Greetings
>
> Florian
>
>
>
>
> ------------------------------------------------------------------------
>  Florian Haberl              Universitaet Erlangen/Nuernberg
>  Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
>
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
>
> ------------------------------------------------------------------------
>
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