[gmx-users] Pull code

[Gavin Melaugh]

Hi all

I am commencing the initial stages for he calculation of potential of
mean force of bringing together two cage molecules. I am following the
tutorial in such an exercise at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
In contrast to the tutorial I want to bring the two molecules together
along the z axis. I have generated an initial configuration in which the
COMs of the two molecules are 5.07 nm apart.
In the tutorial to separate a substrate from a protein you use the
following parameters in the mdp file.

; Pull code
pull            = umbrella
pull_geometry   = distance
pull_dim        = N N Y
pull_start      = yes           ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Chain_B
pull_group1     = Chain_A
pull_rate1      = 0.01          ; 0.01 nm per ps = 10 nm per n
pull_k1         = 1000          ; kJ mol^-1 nm^-


How should I alter this to pull the molecules together along the z axis?
I would've thought the following but I'm not too sure

pull        = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups = 1
pull_group0 = cage_1
pull_group1 = cage_2
pull_rate1 = -0.01
pull_k1 = 1000


Obviously I have to play with the values, but it is the sign that I'm
interested in.

Many Thanks

Gavin