Shortcut: ANGLES

Module	multicolvar
Description	Usage
Calculate functions of the distribution of angles.
output value	type
the ANGLE for each set of three atoms that were specified	vector

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. 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.

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

Calculate functions of the distribution of angles.

This shortcut action allows you to calculate function of a distribution of angles and reproduces the syntax in older PLUMED versions. If you look at the example inputs below you can see how the new syntax operates. We would strongly encourage you to use the newer syntax as it offers greater flexibility.

You can use this command to calculate functions, $g$, such as:

$$f(x) = \sum_{ijk} g( \theta_{ijk} )$$

where $\theta_{ijk}$ is the angle between the vector connecting atom $i$ and and $j$ and the vector connecting atom $j$ and atom $k$. Alternatively you can use this command to calculate functions such as:

$$f(x) = \sum_{ijk} s(r_{ij})s(r_{jk}) g(\theta_{ijk})$$

where $s(r)$ is a switching function. This second form means that you can use this to calculate functions of the angles in the first coordination sphere of an atom / molecule and hence use the CVs described in the paper in the bibliography below.

The following example tells plumed to calculate all angles involving at least one atom from GROUPA and two atoms from GROUPB in which the distances are less than 1.0. The number of angles between $\frac{\pi}{4}$ and $\frac{3\pi}{4}$ is then output

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

a1The ANGLES action with label a1 calculates the following quantities:
 Quantity   
 Type   
 Description  
a1_between
scalar
the number of colvars that have a value that lies in a particular interval: ANGLESCalculate functions of the distribution of angles. This action is a shortcut. More details GROUPAA group of central atoms about which angles should be calculated=1-10 GROUPBWhen used in conjunction with GROUPA this keyword instructs plumed to calculate all distinct angles involving one atom from GROUPA and two atoms from GROUPB=11-100 BETWEENcalculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=0.25pi UPPER=0.75pi} SWITCHthe switching function specifies that only those bonds that have a length that is less than a certain threshold are considered={GAUSSIAN R_0=1.0}
# PLUMED interprets the command:
# a1: ANGLES GROUPA=1-10 GROUPB=11-100 BETWEEN={GAUSSIAN LOWER=0.25pi UPPER=0.75pi} SWITCH={GAUSSIAN R_0=1.0}
# as follows (Click the red comment above to revert to the short version of the input):
The ANGLES action with label a1 calculates the following quantities:
 Quantity   
 Description  
a1.value
the ANGLE for each set of three atoms that were specified
a1.between
the number of colvars that have a value that lies in a particular intervala1: COORD_ANGLESCalculate functions of the distribution of angles between bonds in the first coordination spheres of a set of atoms More details SWITCHthe switching function specifies that only those bonds that have a length that is less than a certain threshold are considered={GAUSSIAN R_0=1.0} CATOMSall the angles between the bonds that radiate out from these central atom are computed=1-10 GROUPa list of angls between pairs of bonds connecting one of the atoms specified using the CATOM command and two of the atoms specified here are computed=11-100  BETWEENcalculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=0.25pi UPPER=0.75pi}
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=a1.between FILEthe name of the file on which to output these quantities=colvar

References

More information about how this action can be used is available in the following articles: - G. A. Tribello, J. Cuny, H. Eshet, M. Parrinello, Exploring the free energy surfaces of clusters using reconnaissance metadynamics. The Journal of Chemical Physics. 135 (2011)

Syntax

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