| This is part of the colvar module |
Calculate the components of the position of an atom.
- Examples
- Glossary of keywords and components
- Description of components
By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.
Quantity | Description |
x | the x-component of the atom position |
y | the y-component of the atom position |
z | the z-component of the atom position |
In addition the following quantities can be calculated by employing the keywords listed below
Quantity | Keyword | Description |
a | SCALED_COMPONENTS | the normalized projection on the first lattice vector of the atom position |
b | SCALED_COMPONENTS | the normalized projection on the second lattice vector of the atom position |
c | SCALED_COMPONENTS | the normalized projection on the third lattice vector of the atom position |
- The atoms involved can be specified using
ATOM | the atom number. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
ATOMS | the atom numbers that you would like to use the positions of. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
- Options
NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |
WHOLEMOLECULES | ( default=off ) if this is a vector of positions do you want to make the positions into a whole before |
SCALED_COMPONENTS | ( default=off ) calculate the a, b and c scaled components of the position separately and store them as label.a, label.b and label.c
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