This is part of the colvar module

Calculate the distance between a pair of atoms.

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.

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 quanties 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

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.

d1:  DISTANCE ATOMS=3,5
d2:  DISTANCE ATOMS=2,4
d2c: DISTANCE ATOMS=2,4 COMPONENTS
PRINT ARG=d1,d2,d2c.x

The following input computes the end-to-end distance for a polymer of 100 atoms and keeps it at a value around 5.

WHOLEMOLECULES ENTITY0=1-100
e2e: DISTANCE ATOMS=1,100 NOPBC
RESTRAINT ARG=e2e KAPPA=1 AT=5

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

WHOLEMOLECULES ENTITY0=1,10,20,30,40,50,60,70,80,90,100
e2e: DISTANCE ATOMS=1,100 NOPBC
RESTRAINT ARG=e2e KAPPA=1 AT=5

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

# this is a center of mass of a large group
c: COM ATOMS=1-100
# this is the distance between atom 101 and the group
d: DISTANCE ATOMS=c,101 COMPONENTS
# 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=d.z PERIODIC=-10,10
# metadynamics on dd
METAD ARG=dz SIGMA=0.1 HEIGHT=0.1 PACE=200

Using SCALED_COMPONENTS this problem should not arise because they are always periodic with domain (-0.5,+0.5).