Action: PLANE
| Module | colvar |
|---|---|
| Description | Usage |
| Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. |   |
Output components
This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.
| Name | Type | Description |
|---|---|---|
| x | scalar/vector | the x-component of the vector that is normal to the plane containing the atoms |
| y | scalar/vector | the y-component of the vector that is normal to the plane containing the atoms |
| z | scalar/vector | the z-component of the vector that is normal to the plane containing the atoms |
Input
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| ATOMS | atoms | the three or four atoms whose plane we are computing |
Further details and examples
Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule.
To calculate the orientation of the plane connecting atoms 1, 2 and 3 you use an input like this:
 |
p: PLANECalculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. More details ATOMSthe three or four atoms whose plane we are computing=1,2,3 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p.x,p.y,p.z FILEthe name of the file on which to output these quantities=colvar
The three components, p.x, p.y and p.z, output by the PLANE action here are the x, y and z components of the normal vector to the plane that is obtained by taking the cross product between the vector connecting atoms 1 and 2 and the vector connecting atoms 2 and 3.
To calculate the cross product of the vector connecting atoms 1 and 2 and the vector connecting atoms 3 and 4 you use an input like this:
|
p: PLANECalculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. More details ATOMSthe three or four atoms whose plane we are computing=1,2,3,4 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p.x,p.y,p.z FILEthe name of the file on which to output these quantities=colvar
If you have multiple molecules and wish to determine the orientations of the planes containing all them with one line of PLUMED input you can use an input like this:
|
p: PLANECalculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. More details ATOMS1the three or four atoms whose plane we are computing=1,2,3 ATOMS2the three or four atoms whose plane we are computing=4,5,6 ATOMS3the three or four atoms whose plane we are computing=7,8,9 ATOMS4the three or four atoms whose plane we are computing=10,11,12 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p.x,p.y,p.z FILEthe name of the file on which to output these quantities=colvar
The output from this command consists of 3 vectors with 4 components. These vectors, p.x, p.y and p.z, contain the x, y and z components of the normals to the planes of the molecules. Commands similar to this are useful for variables that can be used to monitor nucleation of molecular crystals such as SMAC.
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| ATOMS | input | none | the three or four atoms whose plane we are computing |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | optional | false | ignore the periodic boundary conditions when calculating distances |