Evaluating PMF for angle rotations using gmx WHAM
I had been trying to evaluate a PMF using umbrella sampling (GROMACS 2016) for rotating an object. The mdp option I used was:
pull_coord1_geometry = angle-axis
The .mdp options page says the input units are in degrees, and the simulation runs fine with this. However, when evaluating the PMF using gmx WHAM, the histograms seemed to overlap in x space, but not in force space which yields "nan" PMF results.
After troubleshooting, I found that the tpr file input for WHAM is required to be in radians (but is read in degrees within GROMACS simulations) and the pull-f files then can be used to get reasonable PMFs. Right now my workflow is fully functional, but I thought other would like to know how to fix this.
The only fix would be some conversion within WHAM from degrees to radians when reading the tpr files. I hope this helps to continue to improve GROMACS analysis tools