| This is part of the multicolvar module |
Calculate the distance between a pair of atoms in the plane
- 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
GROUP | calculate distance for each distinct set of three atoms in the group. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
VECTORSTART | The first atom position that is used to define the normal to the plane of interest. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
VECTOREND | The second atom position that is used to defin the normal to the plane of interest. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
- 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.
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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... |
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. |