This is part of the analysis module

Calculate the matrix of dissimilarities between a trajectory of atomic configurations.

Glossary of keywords and components
The data to analyze can be the output from another analysis algorithm
USE_OUTPUT_DATA_FROM use the output of the analysis performed by this object as input to your new analysis object
Alternatively data can be collected from the trajectory using
ATOMS the list of atoms that you are going to use in the measure of distance that you are using. For more information on how to specify lists of atoms see Groups and Virtual Atoms
Compulsory keywords
METRIC ( default=EUCLIDEAN ) the method that you are going to use to measure the distances between points
SERIAL ( default=off ) do the calculation in serial. Do not use MPI

( 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...