[gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Dear all,

I follow the Justin’s free energy calculations: Methane in Water tutorial. (Thanks Justin!)
I would like to ask two questions:

1) Is there specific reason to use sd integrator? 
2) Methane molecules is free to sample every x,y,z point in the water bulk. 
    I would like to apply a flat-bottom restraint and keep methane molecule in the centre of bulk.
    I want to prevent methane movement in z direction. 
    Do you have any idea how to remove the effect of flat-bottom restraint afterwards? 

Thanks in advance.
Bests