[gmx-users] pbc = xy

[David L. Bostick]

If this is a monolayer such as those used in, for example, dipole potential
measurement experiments, then it will be natural to have a water-vacuum
interface. If you wish to mimick an experimental setup, will the lipid
tails be attached to a substrate? If so, you may want to tether them with
position restraints.

Typically, in order to simulate such interfaces, you will need to extend
the box along the dimension perpendicular to the monolayer (usually
the z-) plane by approximately 3 times the system size in this dimension.
You can then use PME with a correction term, so called "Ewald 3dc" which
will give you correct electrostatics for slab (2D) boundary conditions.
This correction is built into gromacs, just use the option

ewald_geometry = 3dc

It should work unless the code was taken out. Oh yes... you will need to
use the NVT ensemble so the simulation cell does not collapse, so be sure
the monolayer setup is good ... with the correct area per
surfactant molecule. You will see one or two water molecules escape from
the liquid phase, but don't worry... if you are near ~300K, cohesive forces
will hold everything together.

For an example, see the following reference:

J. Phys. Chem. B. 2000, 104, 5302-5308

Good luck,
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 Wed, 4 May 2005, David wrote:

> On Wed, 2005-05-04 at 11:18 -0230, Jennifer Rendell wrote:
> > Dear Fellow Users,
> >
> > I am modelling a system of a lipid monolayer and water (on the headgroup
> > side). I am considering ways to prevent the water from jumping, via
> > periodic boundary conditions, over to the chain side of the layer.
> >
> > I have had no success using position restraints on a separately
> > defined layer of water near that box side. The water molecules still pop
> > over to the opposite side.
> >
> > How difficult is it to modify the gromacs code to keep periodic boundary
> > conditions in the x and y directions, but not have it in the z direction.
> >
> > Where would I start this kind of modification, if it is feasible?
>
> A simple alternative is to add a vacuum layer by extending the box by
> twice its length.
> >
> > Thank you, Jennifer
> >
> > --
> > Jennifer Rendell
> > Department of Biochemistry
> > Memorial Unversity of Newfoundland
> > St. John's, Newfoundland & Labrador
> >
> > 709-737-6733
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 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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