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This is part of the function module

This function measures the pythagorean distance from a particular structure measured in the space defined by some set of collective variables.

Compulsory keywords
TYPE ( default=EUCLIDEAN ) the manner in which the distance should be calculated
REFERENCE a file in pdb format containing the reference structure. In the PDB file the atomic coordinates and box lengths should be in Angstroms unless you are working with natural units. If you are working with natural units then the coordinates should be in your natural length unit. The charges and masses of the atoms (if required) should be inserted in the beta and occupancy columns respectively. For more details on the PDB file format visit

( default=off ) calculate the derivatives for these quantities numerically