[gmx-users] how to set pull code in gmx 4

[Li Yang]

Dear all

I cannot understand the explanations about settings of pull code in the
gmx 4.

Take a example, there are two particles in the system, and I want to
reproduce the LJ potential using "umbrella sampling".
The settings in gmx 3.3.3 is following:
=====================
..........
runtype = umbrella
ngroups = 1
group_1 = Arg2
reference_group = Arg1
......
pulldim = N N Y
K1 = 700
POS1 = 0 0 1
======================

But I don't know how to set it in gmx 4
Following is the settings in gmx 4:
======================
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella ; ---> "runtype" in gmx 3.3.3
; Pull geometry: distance, direction, cylinder or position
pull_geometry = distance
; Select components for the pull vector. default: Y Y Y
pull_dim = N N Y ; ---> "pulldim" in gmx 3.3.3
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1 = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_start = no
pull_nstxout = 10
pull_nstfout = 1
; Number of pull groups
pull_ngroups = 1 ; ---> "ngroups" in gmx 3.3.3
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0 = Arg2 ; ---> "reference_group" in gmx 3.3.3
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = Arg1 ; ---> "group1" in gmx 3.3.3
pull_weights1 =
pull_pbcatom1 = 0
pull_vec1 = 0.0 0.0 0.0
pull_init1 = 0.0
pull_rate1 = 0
pull_k1 = 700 ; ---> "k1" in gmx 3.3.3
pull_kB1 = 0
======================
if right, which parameter corresponds with "pos1" in gmx3.3.3?

I must apologize in advance if I miss some details in the manual.

Thank you very much

Li Yang