Evaluating PMF for angle rotations using gmx WHAM - Redmine #2609
Archive from user: Jonathan Sheavly
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
(from redmine: issue id 2609, created on 2018-08-14 by gmxdefault, closed on 2019-06-11)
- duplicates #2903 (closed)
- Revision 7e3521c2 by Berk Hess on 2019-06-10T09:43:33Z:
Fix gmx wham with angle geometries Fixes #2609 Change-Id: I36156e1d8bb98499e4357eadc4ca56384da433a5
- Revision 592be1a9 by Berk Hess on 2019-09-30T08:11:47Z:
Actually fix gmx wham with angle geometries A previous fix for converting the force constant in gmx wham for angle and dihedral geometry applied an incorrect conversion factor. Fixes #2609 and #3094 Change-Id: I0aa9b848c7fa62306ccf15b327a650b1ad88e03f