Calculate the z components of the vectors connecting one or many pairs of atoms. You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on.
Examples
The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and the z-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then printed
Click on the labels of the actions for more information on what each action computes
The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and the z-component of the vector connecting atom 1 to atom 2. The number of values that are less than 0.1nm is then printed to a file.
Click on the labels of the actions for more information on what each action computes
The following input tells plumed to calculate the z-components of all the distinct vectors that can be created between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3). The average of these quantities is then calculated.
Click on the labels of the actions for more information on what each action computes
The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB. In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values more than 0.1 is then printed to a file.
Click on the labels of the actions for more information on what each action computes
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.
1.8.17