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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