[gmx-users] Query

[rohit gole]

Dear All,

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

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?

Many Thanks
Rohit

       
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