[gmx-users] PBC only in xy direction

[Michael Brunsteiner]

Andrea Muntean wrote:

> We are using the version 3.3.3. Is there also a posibility to have pbc
> only in xy direction (as I saw it is possible in Gromacs 4.0)? The
> manual says nothing about that.

I don't think this is implemented in 3.3.3 ... but you can just 
make the box length in the z-dimension very large, this gives
about the same effect, if you use PME this might be rather expensive
but you can use a 2-D correction term (which is implemented in version 3.3.3)
then you get at least the physics right (presumably), and in my experience a 
gap of a bit more then the non-bonded cut-off in the z dimension is enough 
to effectively make a 2D-layer behave as if it was alone in time and space.

alternatively you can just install 4.0.2, if gmx is installed system-wide 
where you are you can always install another version of it in your home
directory, that's dead easy unless you have a very exotic hardware or OS.

mic