[gmx-users] Periodic Boundary condition

Rohit merohisg at yahoo.co.in
Mon Feb 4 13:17:35 CET 2008

Hi Mark,
Please accept my apology for not putting a descriptive subject line.
My query is regarding the periodic boundary condition only. I read from email archives regarding implementing periodic boundary conditions in XY plane and not in Z direction and one can do that by increasing the size of box in z direction by 2-3 times and thus creating a vacuum boundary. However, in my case molecules are still moving to other side (i.e -Z) and interacting with the gold surface. But what I want is interaction only at the top surface not the opposite surface. 

I guess now problem is lucid.
Please help me if anything can be done to have a system where molecules can interact only at the top surface of gold layer not the below surface.


Mark Abraham <Mark.Abraham at anu.edu.au> wrote: rohit gole wrote:
> Dear All,

Please use a descriptive subject line so that people can use that to 
work out whether they might be able to help you.

> I am trying to simulate tetrahydrofuran molecules with 3 layer gold surface.
> However, I would like to constrain my system in Z direction. I have 
> tried to do that by increasing the box size in z direction by 3 fold but 
> I still found few molecules coming toward other side. Is there any other 
> way to implement the boundary conditions only in XY plane? 

I'm afraid I don't understand this description of what you're trying to 
do. Please have a read of the manual sections on *restraints* (not 

> or to have a 
> repulsive wall potential at some z?

That's not implemented.

> And is it possible to place the system at the z=0 plane instead of 
> having it at the center of simulation box either by using editconf or 
> some other?

No, but you can use trjconv after the simulation to get various effects. 
It's just a translation anyway....

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