[gmx-users] umbrella sampling in gromacs

[Gard Nelson]

Hi all,
I'd like to calculate the PMF for a small molecule moving from a
membrane-bound protein into the membrane itself.  I tried using the
"cylinder" option for pull_geometry, but when I tried to analyze the results
with g_wham it said that "cylinder" isn't a supported option.  Is this
correct?  Is there anything I can do to still use this geometry?

If it won't work, I thought maybe I could instead use "distance" for
pull_geometry, and then restrict pull_dim to the z axis (N N Y, right?).
 I'm worried that if I do this and the centers of mass of my molecule and
the bilayer don't align, then the umbrella potential will still be directed
along the vector connecting the two COMs and the Z-component of the
potential will therefore be something smaller (dependent on the angle
between the COM-COM vector and the z axis).  Does anyone know how this is
implemented?

Thanks,
Gard
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