[gmx-developers] walls and pbc setting in CVS code

Makoto Yoneya makoto-yoneya at aist.go.jp
Tue Jul 15 16:06:49 CEST 2008

Dear GROMACS developers:

I'd tried the walls function in the CVS code and found works well.
In the current implementation, the walls function can only be used with
pbc=xy as in the online manual.
However, I'd like to use the walls without the pbc=xy setting (i.e.
the common 3-D pbc).
I'm considering a Langmuir monolayer (monolayer on a water layer) and trans
monolayer water (in Z-direction from the water
layer) simulation.
The water layer may be modeled with the wall function with the 9-3
The trans monolayer water vapor flow (in Z-direction) may be modeled with
energygrp_excl: VAPOR_WATER wall0
acc_grps: VAPOR_WATER
accelerate: 0.0 0.0 0.5.
So, the water molecules may flow periodically in Z-direction (then requires
3-D pbc).

If these may work, then please consider to work the walls function even
without pbc=xy.

Thank you for advance.

Makoto Yoneya, Dr.
AIST, Japan

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