[gmx-users] Query

Mark Abraham Mark.Abraham at anu.edu.au
Mon Feb 4 12:04:51 CET 2008

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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