Closed HanatoK closed 5 years ago
Very good question. The reason is that is makes it easier to use a histogram-based estimator after eABF. Such estimators (like CZAR) rely on the histogram of the actual CV. If the wall potential is applied to the extended coordinate, then it "bleeds" into the distribution of the actual CV, giving a wrong free energy gradient near the wall.
@jhenin Thanks for your answer!
Very good question. The reason is that is makes it easier to use a histogram-based estimator after eABF. Such estimators (like CZAR) rely on the histogram of the actual CV. If the wall potential is applied to the extended coordinate, then it "bleeds" into the distribution of the actual CV, giving a wrong free energy gradient near the wall.
@jhenin What about letting CZAR support the "expandBoundaries" ? Occationally I found adding wall potential on the actual CV leads to strange performance in meta-eABF and extended-Lagrangian-based metadynamics.
@jhenin can reply on whether it's appropriate to port expandBoundaries
to ABF: right now, it's pretty much contained in colvarbias_meta::update_grid_params()
.
However, I'm missing the connection with the wall potentials.
I think the problem with expandBoundaries is that it would make the sampling histogram decay to zero at the boundaries, which is acceptable for single-window sampling but not really for stratified sampling, where you want accurate free energy derivatives all the way to the boundaries.
I am a little curious about the harmonic walls implementation with extended Lagrangian dynamics. Is applying the wall potential to actual CVs theoretically better than to extended CVs?