[gmx-users] questions about umbrella sampling

[凌未风]

Hello everyone:

I am trying to do PMF calculation by umbrella sampling, and I would like to control the distance between two lipid molecules on the plane of membrane bilayer (i.e., the x-y plane). I have a question of how to implement it in gromacs, because in gromacs, if we are doing umbrella sampling, we have to use the pulling code as follows:

pull            = umbrella
pull-geometry   = distance  ; simple distance increase 
pull-dim        = Y Y N
pull-vec1       = 0 0 0
pull-start      = yes       ; define initial COM distance > 0
pull-ngroups    = 1
pull-group0     = group0 
pull-group1     = group1
pull-rate1      = 0.001         ; pull rate, 6nm finished in 60ns
pull-nstxout    = 500
pull-nstfout    = 500
pull-k1         = 4500      ; kJ mol^-1 nm^-2 ; try smaller one, 

when we try to pull the two groups away, we have to define the direction of the pulling force. 
My question is: how to define "pull-dim" and "pull-vec1" if I would like to control the distance between the center of mass of two lipid molecules on the membrane plane. In my case I have to control the distance on the x-y plane, which is sqrt(x^2+y^2). How could we do this in gromacs?
If we would like to control the distance in on direction, e.g., the distance along the z direction, it is straightforward, we could define pull-dim= N N Y, and pull-vec1=0 0 1. But in my case how could we do it? Or we have to use plumed package to implement it?

Thanks for your help. Look forwarding to hearing from someone. 

With my best regards, 
RXG