Shortcut: ZYTORSIONS

Module	multicolvar
Description	Usage
Calculate the torsional angle around the z axis between an arbitrary vector and the positive y direction
output value	type
the angle between the vector connecting each pair of atoms and the the positive X/Y/Z direction around the X/Y/Z axis	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.

Name	Type	Keyword	Description
lessthan	scalar	LESS_THAN	the number of colvars that have a value less than a threshold
morethan	scalar	MORE_THAN	the number of colvars that have a value more than a threshold
altmin	scalar	ALT_MIN	the minimum value of the cv
min	scalar	MIN	the minimum colvar
max	scalar	MAX	the maximum colvar
between	scalar	BETWEEN	the number of colvars that have a value that lies in a particular interval
highest	scalar	HIGHEST	the largest of the colvars
lowest	scalar	LOWEST	the smallest of the colvars
sum	scalar	SUM	the sum of the colvars
mean	scalar	MEAN	the mean of the colvars

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 pairs of atoms that you would like to calculate the angles for

Further details and examples

Calculate the torsional angle around the z axis between an arbitrary vector and the positive y direction

The following input tells plumed to calculate the angle around the z direction between the positive y-axis and the vector connecting atom 3 to atom 5 and the angle around the z direction between the positive y-axis and the vector connecting atom 1 to atom 2. The average of these two quantities is then output

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

d1The ZYTORSIONS action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the angle between the vector connecting each pair of atoms and the the positive X/Y/Z direction around the X/Y/Z axis
d1_mean scalar the mean of the colvars: ZYTORSIONSCalculate the torsional angle around the z axis between an arbitrary vector and the positive y direction This action is a shortcut. More details ATOMS1the pairs of atoms that you would like to calculate the angles for=3,5 ATOMS2the pairs of atoms that you would like to calculate the angles for=1,2 MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# d1: ZYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MEAN
# as follows (Click the red comment above to revert to the short version of the input):
d1_originThe FIXEDATOM action with label d1_origin calculates the following quantities: Quantity    Type    Description  
d1_origin atoms virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0,0,0
d1_axisThe FIXEDATOM action with label d1_axis calculates the following quantities: Quantity    Type    Description  
d1_axis atoms virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0,0,1
d1_vec2The FIXEDATOM action with label d1_vec2 calculates the following quantities: Quantity    Type    Description  
d1_vec2 atoms virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0,1,0
d1The TORSION action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 vector the TORSION for each set of specified atoms: TORSIONCalculate one or multiple torsional angles. More details VECTORA1two atoms that define a vector=3,5 VECTORB1two atoms that define a vector=d1_vec2,d1_origin AXIS1two atoms that define an axis=d1_axis,d1_origin VECTORA2two atoms that define a vector=1,2 VECTORB2two atoms that define a vector=d1_vec2,d1_origin AXIS2two atoms that define an axis=d1_axis,d1_origin
d1_meanThe MEAN action with label d1_mean calculates the following quantities: Quantity    Type    Description  
d1_mean scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=d1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- 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=d1_mean

Notice that this command is a shortcut. You can thus learn more about how to use PLUMED by examining the expanded version of the input above.

Syntax

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

Keyword	Type	Default	Description
ATOMS	input	none	the pairs of atoms that you would like to calculate the angles for
LESS_THAN	optional	not used	calculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.
MORE_THAN	optional	not used	calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.
ALT_MIN	optional	not used	calculate the minimum value
MIN	optional	not used	calculate the minimum value
MAX	optional	not used	calculate the maximum value
BETWEEN	optional	not used	calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.
HIGHEST	optional	false	this flag allows you to recover the highest of these variables
HISTOGRAM	optional	not used	calculate a discretized histogram of the distribution of values
LOWEST	optional	false	this flag allows you to recover the lowest of these variables
SUM	optional	false	calculate the sum of all the quantities
MEAN	optional	false	calculate the mean of all the quantities

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Quantity	Type	Description
d1	vector	the angle between the vector connecting each pair of atoms and the the positive X/Y/Z direction around the X/Y/Z axis
d1_mean	scalar	the mean of the colvars