[gmx-users] Periodic Boundary condition

Mark Abraham Mark.Abraham at anu.edu.au
Mon Feb 4 13:32:00 CET 2008

Rohit wrote:
> 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.

This suggests that your system size is small enough that your long-range 
non-bonded interactions and/or velocities are big enough that you can 
traverse the vacuum gap. Is your physical model comparable with 
published studies? If not, check there first.  Other than increasing 
your gap or playing with your physics, there's not much one can suggest. 
You could use distance restraints on all particles that keep them within 
a certain distance of an atom the surface, but this might be problematic 
if the surface's area is large with respect to the restraint distance. 
I'd much rather fix my physics than do this, however.

> 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.


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