This is part of the analysis module

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

Glossary of keywords and components
The data to analyze can be the output from another analysis algorithm
ATOMS the atoms whose positions we are tracking for the purpose of analyzing the data
STRIDE the frequency with which data should be stored for analysis. By default data is collected on every step
Compulsory keywords
CLEAR ( default=0 ) the frequency with which data should all be deleted and restarted

( default=off ) lower the memory requirements

ARG the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...
LOGWEIGHTS list of actions that calculates log weights that should be used to weight configurations when calculating averages