MAZE_LOSS
 This is part of the maze module It is only available if you configure PLUMED with ./configure –enable-modules=maze . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Define a coarse-grained loss function describing interactions in a ligand-protein complex, which is minimized during the simulation to obtain ligand unbinding pathways.

The loss function is the following:

$\mathcal{L}= \sum_{i=1}^{N_p} r_i^{-\alpha}\text{e}^{-\beta r_i^{-\gamma}},$

where $$N_p$$ is the number of ligand-protein atom pairs, $$r$$ is a re-scaled distance between the $$i$$th pair, and $$\alpha, \beta, \gamma$$ are the positive parameters defined in that order by the PARAMS keyword.

Examples

The loss function can be defined in the following way:

Click on the labels of the actions for more information on what each action computes
l: MAZE_LOSS PARAMScompulsory keyword
Parameters for the loss function. =1,1,1

Glossary of keywords and components
Compulsory keywords
 PARAMS Parameters for the loss function.
Options
 NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances