YANGLES
This is part of the multicolvar module

Calculate the angle between an arbitrary vector and the positive y direction

Examples
Glossary of keywords and components
Description of components
Quantity Keyword Description
lessthan LESS_THAN the number of colvars that have a value less than a threshold
morethan MORE_THAN the number of colvars that have a value more than a threshold
altmin ALT_MIN the minimum value of the cv
min MIN the minimum colvar
max MAX the maximum colvar
between BETWEEN the number of colvars that have a value that lies in a particular interval
highest HIGHEST the largest of the colvars
lowest LOWEST the smallest of the colvars
sum SUM the sum of the colvars
mean MEAN the mean of the colvars
The atoms involved can be specified using
ATOMS the pairs of atoms that you would like to calculate the angles for. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3...
Options
HIGHEST ( default=off ) this flag allows you to recover the highest of these variables.
LOWEST ( default=off ) this flag allows you to recover the lowest of these variables.
SUM ( default=off ) calculate the sum of all the quantities.
MEAN

( default=off ) calculate the mean of all the quantities.

LESS_THAN calculate the number of variables that are less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3...
MORE_THAN calculate the number of variables that are more than a certain target value. This quantity is calculated using \(\sum_i 1 - \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. MORE_THAN1, MORE_THAN2, MORE_THAN3...
ALT_MIN calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = -\frac{1}{\beta} \log \sum_i \exp\left( -\beta s_i \right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)).
MIN calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) } \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\))
MAX calculate the maximum value. To make this quantity continuous the maximum is calculated using \( \textrm{max} = \beta \log \sum_i \exp\left( \frac{s_i}{\beta}\right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\))
BETWEEN calculate the number of values that are within a certain range. These quantities are calculated using kernel density estimation as described on histogrambead.. You can use multiple instances of this keyword i.e. BETWEEN1, BETWEEN2, BETWEEN3...
HISTOGRAM calculate a discretized histogram of the distribution of values. This shortcut allows you to calculates NBIN quantites like BETWEEN.