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

Makoto Yoneya makoto-yoneya at aist.go.jp
Tue Jul 22 04:17:17 CEST 2008

Dear Prof. Berk Hess and GROMACS developers:

Thanks a lot for your reply and the precious info.
Sorry for my bad explanations.
I simply want to simulate the system with a water layer
(modeled by a wall) and a monolayer on it.
So far the system can simulate with original CVS code.
However, I also want to add trans-monolayer constant vapor flow
(in Z-direction) of water molecules from the water layer
(wall) to the system above.
I'll try the code modifications and check the result.

Best regards,

Makoto Yoneya, Dr.
AIST Japan

> Hello,
>I don't understand exactly what you want to do.
>But if you are really convinced that it makes sense for your research,
>you can modify the code.
>In src/kernel/readir.c you have to comment out the line:
>  CHECK(ir->nwall && ir->ePBC!=epbcXY);
>and recompile grompp.
>Makoto Yoneya wrote:
> 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
> monolayer water (in Z-direction from the water
> layer) simulation.
> The water layer may be modeled with the wall function with the 9-3
> potential.
> The trans monolayer water vapor flow (in Z-direction) may be modeled with
> specifying,
> energygrp_excl: VAPOR_WATER wall0
> and
> acc_grps: VAPOR_WATER
> accelerate: 0.0 0.0 0.5.
> So, the water molecules may flow periodically in Z-direction (then
> 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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