Action: ANGLE

Module	colvar
Description	Usage
Calculate one or multiple angle/s.
output value	type
the ANGLE involving these atoms	scalar/vector

Details and examples

Calculate one or multiple angle/s.

The following input instructs PLUMED to calculate and print the angle between the vector connecting atom 2 and atom 1 and the vector connecting atom 2 and atom 3.

Click on the labels of the actions for more information on what each action computes

a1The ANGLE action with label a1 calculates the following quantities: Quantity    Type    Description  
a1 scalar the ANGLE involving these atoms: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1,2,3
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=a1 FILEthe name of the file on which to output these quantities=colvar

In other words, the angle that is output by the input above is calculated as:

$\theta=\arccos\left(\frac{ r_{21}\cdot r_{23}}{ | r_{21}| | r_{23}|}\right)$

Here $r_{ij}$ is the vector connecting the $i$ th and $j$ th atoms, which by default is evaluated in a way that takes periodic boundary conditions into account. If you wish to disregard the PBC you can use the NOPBC flag as shown in the following input:

Click on the labels of the actions for more information on what each action computes

a1The ANGLE action with label a1 calculates the following quantities: Quantity    Type    Description  
a1 scalar the ANGLE involving these atoms: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1,2,3 NOPBC ignore the periodic boundary conditions when calculating distances
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=a1 FILEthe name of the file on which to output these quantities=colvar

If the NOPBC flag is not included any sets of atoms that are broken by the periodic boundaries are made whole using a procedure that is the same as that described in the documentation for WHOLEMOLECULES.

We can also instruct PLUMED to calculate the angle between the vectors connecting atoms 1 and atom 2 and atoms 3 and atom 4 by using the following input:

Click on the labels of the actions for more information on what each action computes

a3The ANGLE action with label a3 calculates the following quantities: Quantity    Type    Description  
a3 vector the ANGLE for each set of specified atoms: ANGLECalculate one or multiple angle/s. More details ATOMS1the list of atoms involved in this collective variable (either 3 or 4 atoms)=1,2,3 ATOMS2the list of atoms involved in this collective variable (either 3 or 4 atoms)=4,5,6 ATOMS3the list of atoms involved in this collective variable (either 3 or 4 atoms)=7,8,9
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=a3 FILEthe name of the file on which to output these quantities=colvar

It is common to assume when using this feature that all the angles being computed are indistinguishable so it makes sense to perform the same series of operations on every element of the output vector. The input file below is more approrpriate if the angles are not indistinguishable:

Click on the labels of the actions for more information on what each action computes

a4The ANGLE action with label a4 calculates the following quantities: Quantity    Type    Description  
a4 scalar the ANGLE involving these atoms: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1,2,3
a5The ANGLE action with label a5 calculates the following quantities: Quantity    Type    Description  
a5 scalar the ANGLE involving these atoms: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=4,5,6
a6The ANGLE action with label a6 calculates the following quantities: Quantity    Type    Description  
a6 scalar the ANGLE involving these atoms: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=7,8,9
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=a4,a5,a6 FILEthe name of the file on which to output these quantities=colvar

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 list of atoms involved in this collective variable (either 3 or 4 atoms)

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ATOMS	input	none	the list of atoms involved in this collective variable (either 3 or 4 atoms)
NOPBC	optional	false	ignore the periodic boundary conditions when calculating distances

Quantity	Type	Description
a1	scalar	the ANGLE involving these atoms