In gromacs umbrella sampling as it mentioned in pull code that pull along the z co-ordinate , but in my case the molecules pulling over the protein is not in a x axis ,y axis and z axis .it should be pull in between the x and y axis so how can i re frame my pull code
The pull coordinate directions in GROMACS can be in any linear direction, e.g. see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-pull-coord1-vec.
So, e.g. if you want to pull coordinate 2 in the direction between the x and y axis, then use
pull-coord2-vec = 1.0, 1.0, 0.0