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.

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

Examples

The loss function can be defined in the following way:

l: MAZE_LOSS PARAMS=1,1,1