DISTANCES

This is part of the multicolvar module |

Calculate the distances between multiple piars of atoms

- Examples

- Glossary of keywords and components

- Description of components

Quantity | Description |

.#!value | the DISTANCES between the each pair of atoms that were specified |

In addition the following quantities can be calculated by employing the keywords listed below

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 |

x | COMPONENTS | the x-components of the distance vectors |

y | COMPONENTS | the y-components of the distance vectors |

z | COMPONENTS | the z-components of the distance vectors |

- The atoms involved can be specified using

GROUP | Calculate the distance between each distinct pair of atoms in the group |

- Or alternatively by using

GROUPA | Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB. This must be used in conjunction with GROUPB. |

GROUPB | Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB. This must be used in conjunction with GROUPA. |

- Or alternatively by 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... |

ORIGIN | calculate the distance of all the atoms specified using the ATOMS keyword from this point. For more information on how to specify lists of atoms see Groups and Virtual Atoms |

LOCATION | the location at which the CV is assumed to be in space. You can use multiple instances of this keyword i.e. LOCATION1, LOCATION2, LOCATION3... |

- Options

NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |

COMPONENTS | ( default=off ) calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z |

SCALED_COMPONENTS | ( default=off ) calculate the a, b and c scaled components of the distance separately and store them as label.a, label.b and label.c |

LOWMEM | ( default=off ) this flag does nothing and is present only to ensure back-compatibility |

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. |