[gmx-users] Question about umbrella sampling through a nanotube

[chris.neale at utoronto.ca]

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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