By default the distance is computed taking into account periodic boundary conditions. This behavior can be changed with the NOPBC flag. Moreover, single components in Cartesian space (x,y, and z, with COMPONENTS) or single components projected to the three lattice vectors (a,b, and c, with SCALED_COMPONENTS) can be also computed.
Notice that Cartesian components will not have the proper periodicity! If you have to study e.g. the permeation of a molecule across a membrane, better to use SCALED_COMPONENTS.
Examples
The following input tells plumed to print the distance between atoms 3 and 5, the distance between atoms 2 and 4 and the x component of the distance between atoms 2 and 4.
Click on the labels of the actions for more information on what each action computes
the pair of atom that we are calculating the distance between.
=3,5 The DISTANCE action with label d1 calculates a single scalar valued2: DISTANCE
ATOMS
the pair of atom that we are calculating the distance between.
=2,4 The DISTANCE action with label d2 calculates a single scalar valued2c: DISTANCE
ATOMS
the pair of atom that we are calculating the distance between.
=2,4
COMPONENTS
( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x,
The DISTANCE action with label d2c calculates the following quantities:
Quantity
Description
d2c.x
the x-component of the vector connecting the two atoms
d2c.y
the y-component of the vector connecting the two atoms
d2c.z
the z-component of the vector connecting the two atoms
The following input computes the end-to-end distance for a polymer of 100 atoms and keeps it at a value around 5.
Click on the labels of the actions for more information on what each action computes
Notice that NOPBC is used to be sure that if the end-to-end distance is larger than half the simulation box the distance is compute properly. Also notice that, since many MD codes break molecules across cell boundary, it might be necessary to use the WHOLEMOLECULES keyword (also notice that it should be before distance). The list of atoms provided to WHOLEMOLECULES here contains all the atoms between 1 and 100. Strictly speaking, this is not necessary. If you know for sure that atoms with difference in the index say equal to 10 are not going to be farther than half cell you can e.g. use
Click on the labels of the actions for more information on what each action computes
Just be sure that the ordered list provide to WHOLEMOLECULES has the following properties:
Consecutive atoms should be closer than half-cell throughout the entire simulation.
Atoms required later for the distance (e.g. 1 and 100) should be included in the list
The following example shows how to take into account periodicity e.g. in z-component of a distance
Click on the labels of the actions for more information on what each action computes
the list of atoms which are involved the virtual atom's definition.
=1-100 The COM action with label c calculates the following quantities:
Quantity
Description
c.x
the x coordinate of the virtual atom
c.y
the y coordinate of the virtual atom
c.z
the z coordinate of the virtual atom
c.mass
the mass of the virtual atom
c.charge
the charge of the virtual atom
# this is the distance between atom 101 and the groupd: DISTANCE
ATOMS
the pair of atom that we are calculating the distance between.
=c,101
COMPONENTS
( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x,
The DISTANCE action with label d calculates the following quantities:
Quantity
Description
d.x
the x-component of the vector connecting the two atoms
d.y
the y-component of the vector connecting the two atoms
d.z
the z-component of the vector connecting the two atoms
# this makes a new variable, dd, equal to d and periodic, with domain -10,10# this is the right choise if e.g. the cell is orthorombic and its size in# z direction is 20.dz: COMBINE
ARG
the input to this function.
=d.z
PERIODIC
compulsory keyword
if the output of your function is periodic then you should specify the periodicity
of the function.
=-10,10 The COMBINE action with label dz calculates a single scalar value# metadynamics on dd
Using SCALED_COMPONENTS this problem should not arise because they are always periodic with domain (-0.5,+0.5).
Glossary of keywords and components
Description of components
By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.
Quantity
Keyword
Description
x
COMPONENTS
the x-component of the vector connecting the two atoms
y
COMPONENTS
the y-component of the vector connecting the two atoms
z
COMPONENTS
the z-component of the vector connecting the two atoms
a
SCALED_COMPONENTS
the normalized projection on the first lattice vector of the vector connecting the two atoms
b
SCALED_COMPONENTS
the normalized projection on the second lattice vector of the vector connecting the two atoms
c
SCALED_COMPONENTS
the normalized projection on the third lattice vector of the vector connecting the two atoms
The atoms involved can be specified using
ATOMS
the pair of atom that we are calculating the distance between. For more information on how to specify lists of atoms see Groups and Virtual Atoms
Options
NUMERICAL_DERIVATIVES
( default=off ) calculate the derivatives for these quantities numerically
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