[gmx-users] Re: question of smd

[Thomas Schlesier]

Think the best way to do this, is making the box in z-direction very 
long, searching for atoms/groups of your ligand which should be parallel 
to the z-axis, put them in an index group and then use 'editconf -princ'

But why would you want to have your ligand along the z-axis?!?
You can also pull the ligand in 3D instead of 1D (along z-axis).

Greetings
Thomas

 >Dear GMX users,
 >
 >I want to do calculations of PMF based SMD and US, for the SMD 
 >calculation, first I should change the coordinates of the protein and 
 >ligand, so that the orientation of the ligand is parallel with Z axis. 
 >Could someone tell me how to deal with this step? Thanks very much!
 >
 >All the best,
 >qinghua