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

Compulsory keywords

ARG

the input for this action is the output from one or more other actions. The particular output that you used is referenced using that action of interests label. If the label appears on its own then the value of the relevant Action is taken. If * or *.* appears the information from all arguments is taken. Some actions have multi-component outputs, each component of the output has a specific label so for instance an action labelled dist may have three componets 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.*

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 http://www.wwpdb.org/docs.html

Options

NUMERICAL_DERIVATIVES

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

REFERENCE_VEC

the vector of values for the CVs at the reference point (if you use this you don't need REFERENCE)

Examples