CV:OPOS2

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Navigation: Documentation / Collective Variables / CV:OPOS2


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Definition

The absolute position of the point along a selected axis of the superimposed coordinate system of a reference structure. Any axis of the superimposed coordinate system can be selected.

Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \xi_{x} = A_{com,x}^'}
Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \xi_{y} = A_{com,y}^'}
Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \xi_{z} = A_{com,z}^'}

The relation between re-oriented (') and native coordinate system is given by the transformation matrix T:

Failed to parse (Conversion error. Server ("cli") reported: "[INVALID]"): {\displaystyle \bold A_{com}^' = \bold T \bold A_{com}}


Specification

Section name: OPOS2

Key Type Default Description




name string unique CV name
group_a mask atoms specifying the point A
reference_a string name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_a
group_b mask atoms specifying the point B
direction x, y, z select axis in the superimposed coordinate system

Keys in bold are mandatory.