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 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.