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 
PARAMS
compulsory keyword 
Parameters for the loss function. 
=1,1,1 The MAZE_LOSS action with label l

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
.#!value	the value of the loss function

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