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

This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object

Examples

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. 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
data	the data that is being collected by this action
logweights	the logarithms of the weights of the data points

Compulsory keywords

STRIDE	( default=1 ) the frequency with which data should be stored for analysis. By default data is collected on every step
CLEAR	( default=0 ) the frequency with which data should all be deleted and restarted
ALIGN	( default=OPTIMAL ) if storing atoms how would you like the alignment to be done can be SIMPLE/OPTIMAL

Options

ARG	the arguments you would like to collect
ATOMS	list of atomic positions that you would like to collect and store for later analysis
LOGWEIGHTS	list of actions that calculates log weights that should be used to weight configurations when calculating averages