Umbrella Sampling: Dimension of Reaction Coordinate

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GROMACS version:2020.6
GROMACS modification: Yes
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Hi,

I’m trying to undertstand how Umbrella sampling/WHAM analysis works. If I have:

pull_coord1_dim = Y Y N ; RC is X distance

which as I understand adds biasing potential on both X and Y coordinates, does that make my reaction coordinate 2D (even in the absence of a second pull group)?

Following that, how does wham handle high dimensional RC?What does it mean that “all pull coordinates found in all pullx/pullf files are used in WHAM“ (from gmx wham)? I tried supplying a three-distance RC, but it still computed a 1D PMF, shouldn’t it be a 3D PMF?

Thank you.

2

If coord1 is your only coordinate, it is 1D. For 2D you would need to add pull_coord2. What you pull coordinate geometry is is defined by pull_coord1_geometry, which you don’t list above.