Unfortunately, I don't think that there is any way to use this data
(and only this data) to derive the PMF along z. The way that you did
your US, the PMF along z is convoluted with xy motion. You can get the
PMF along the reaction coordinate that you actually used (XYZ) using
standard WHAM and try to interpret it, I suppose. In your special
case, there is probably a mathematical conversion between the XYZ PMF
and the Z-only PMF due to the symmetry of the system.
What one would desire is two separate restraints, one operating in Z
and one operating in XY. That is, unfortunately, not possible in the
standard version of gromacs.
-- original message --
Dear GMXers,
I'm trying to compute the PMF of a molecule along the centerline of a
nanotube (the axial direction of the nanotube is parallel to the z axis).
The nanotube is used as the reference group and the molecule as the pulling
group.
pull_geometry = position
pull_dim = Y Y Y
pull_start = no
pull_init1 = 0 0 1.2
pull_rate1 = 0.00
pull_k1 = 1000
pull_nstxout = 1000
pull_nstfout = 1000
"pull_dim=Y Y Y" is used to make sure that the molecule is always close to
the centerline of the nanotube.
From the output of "pullx.xvg", the COM positions in all three directions
(i.e. x,y,z) are included.
How to get the PMF only along z axis from here? Is it OK if I just take the
corresponding z column and do g_wham directly?
Thank you.
Best,
Yanbin
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