| This is part of the multicolvar module |
Calculate all the angles between bonds in the first coordination spheres of a set of atoms
- 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 |
between | BETWEEN | the number of colvars that have a value that lies in a particular interval |
sum | SUM | the sum of the colvars |
mean | MEAN | the mean of the colvars |
- The atoms involved can be specified using
CATOMS | all the angles between the bonds that radiate out from these central atom are computed. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
GROUP | a 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. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
- Compulsory keywords
SWITCH | the switching function specifies that only those bonds that have a length that is less than a certain threshold are considered |
- Options
SUM | ( default=off ) calculate the sum of all the quantities. |
MEAN | ( default=off ) calculate the mean of all the quantities.
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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... |
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. |