2D periodic boundary condn & PME

From: Harindar Keer (hkeer_at_uci.edu)
Date: Tue Jun 17 2008 - 14:12:28 CDT

Dear all,

  I need to simulate a system, described below, with periodic boundary
conditions applied only in two directions , X & Y. I can not use PME
with such periodic boundary condition. But simulation runs fine without
PME, I am wondering in this case how full electrostatics is being
treated and its cost. I would like to seek advice on how best to set up,
parameters etc. , such a system for simulation, or any other suggestions
you might have. Thanks for your time.

Regards,
Harindar

Schematic of the system:

^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ }
^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ } water layer
^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ }
^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ }
 o o o o o o o o o o o o o ] Z
      Y
 | | | | | | | | | | | | | | | | ]
                    | /
 | | | | | | | | | | | | | | | | ]
                      | /
                                                ] Lipids
          | /
| | | | | | | | | | | | | | | | ]
                     --------> X
| | | | | | | | | | | | | | | | ]
o o o o o o o o o o o o o ]
~~~~~~~~~~~~~~~~~~~~~~~ <- surface

periodic boundary conditons applied in X & Y direction only.

>Error if apply PME with 2d periodic boundary condn:
PME requires periodic boundary conditions.

Snippet from configuration file:
if {1} {
cellBasisVector1 260 0. 0.
cellBasisVector2 0. 110 0.
cellOrigin 0 0. 21.
}

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 256
PMEGridSizeY 128
PMEGridSizeZ 128
}

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