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