[gmx-users] Question about umbrella sampling "pull-geometry" option

[WU Yanbin]

Dear GMXers,

I'm running umbrella PMF calculations using GROMACS 4.5. A molecule is
placed at various locations of a channel to compute the energy barrier of
the entrance.

Below is the PMF section of mdp input, to compute the PMF around the
position of (4.04700, 4.0582, -2.2058). The pulling molecule is initially
placed close to the (4.04700, 4.0582, -2.2058) position.
The box size is 8.094*8.1164*6.0. The series of positions I considered is in
the z-coordinate range of -2.2 to -0.8.

-----------------------
pull            = umbrella
pull_geometry   = position
pull_dim        = N N Y
pull_start      = no
pull_ngroups    = 1
pull_group0     =
pull_group1     = MOL1
pull_init1      = 4.04700  4.05820   -2.2058
pull_rate1      = 0.00
pull_k1         = 1000
pull_nstxout    = 1000
pull_nstfout    = 1000
-----------------------

For this particular configuration, should I use "pull-geometry=position" or
"pull-geometry=distance"? Or they are the same for this case?
I read the manual and PMF tutorial but cannot figure this out. Could anyone
provide more details about this?

Thank you.

Best,
Yanbin
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