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Subsections

## Distances

### distance: center-of-mass distance between two groups.

The distance {...} block defines a distance component between the two atom groups, group1 and group2.

• group1 First group of atoms
Context: distance
Acceptable values: Block group1 {...}
Description: First group of atoms.

• group2: analogous to group1

• forceNoPBC Calculate absolute rather than minimum-image distance?
Context: distance
Acceptable values: boolean
Default value: no
Description: By default, in calculations with periodic boundary conditions, the distance component returns the distance according to the minimum-image convention. If this parameter is set to yes, PBC will be ignored and the distance between the coordinates as maintained internally will be used. This is only useful in a limited number of special cases, e.g. to describe the distance between remote points of a single macromolecule, which cannot be split across periodic cell boundaries, and for which the minimum-image distance might give the wrong result because of a relatively small periodic cell.

• oneSiteTotalForce Measure total force on group 1 only?
Context: angle, dipoleAngle, dihedral
Acceptable values: boolean
Default value: no
Description: If this is set to yes, the total force is measured along a vector field (see equation (13.25) in section ) that only involves atoms of group1. This option is only useful for ABF, or custom biases that compute total forces. See section  for details.

The value returned is a positive number (in Å), ranging from 0 to the largest possible interatomic distance within the chosen boundary conditions (with PBCs, the minimum image convention is used unless the forceNoPBC option is set).

### distanceZ: projection of a distance vector on an axis.

The distanceZ {...} block defines a distance projection component, which can be seen as measuring the distance between two groups projected onto an axis, or the position of a group along such an axis. The axis can be defined using either one reference group and a constant vector, or dynamically based on two reference groups. One of the groups can be set to a dummy atom to allow the use of an absolute Cartesian coordinate.

• main Main group of atoms
Context: distanceZ
Acceptable values: Block main {...}
Description: Group of atoms whose position is measured.

• ref Reference group of atoms
Context: distanceZ
Acceptable values: Block ref {...}
Description: Reference group of atoms. The position of its center of mass is noted below.

• ref2 Secondary reference group
Context: distanceZ
Acceptable values: Block ref2 {...}
Default value: none
Description: Optional group of reference atoms, whose position can be used to define a dynamic projection axis: . In this case, the origin is , and the value of the component is .

• axis Projection axis (Å)
Context: distanceZ
Acceptable values: (x, y, z) triplet
Default value: (0.0, 0.0, 1.0)
Description: The three components of this vector define a projection axis for the distance vector joining the centers of groups ref and main. The value of the component is then . The vector should be written as three components separated by commas and enclosed in parentheses.

• forceNoPBC: see definition of forceNoPBC (distance component)

• oneSiteTotalForce: see definition of oneSiteTotalForce (distance component)
This component returns a number (in Å) whose range is determined by the chosen boundary conditions. For instance, if the axis is used in a simulation with periodic boundaries, the returned value ranges between and , where is the box length along (this behavior is disabled if forceNoPBC is set).

### distanceXY: modulus of the projection of a distance vector on a plane.

The distanceXY {...} block defines a distance projected on a plane, and accepts the same keywords as the component distanceZ, i.e. main, ref, either ref2 or axis, and oneSiteTotalForce. It returns the norm of the projection of the distance vector between main and ref onto the plane orthogonal to the axis. The axis is defined using the axis parameter or as the vector joining ref and ref2 (see distanceZ above).

• main: see definition of main (distanceZ component)
• ref: see definition of ref (distanceZ component)
• ref2: see definition of ref2 (distanceZ component)
• axis: see definition of axis (distanceZ component)
• forceNoPBC: see definition of forceNoPBC (distance component)
• oneSiteTotalForce: see definition of oneSiteTotalForce (distance component)

### distanceVec: distance vector between two groups.

The distanceVec {...} block defines a distance vector component, which accepts the same keywords as the component distance: group1, group2, and forceNoPBC. Its value is the 3-vector joining the centers of mass of group1 and group2.

• group1: see definition of group1 (distance component)
• group2: analogous to group1
• forceNoPBC: see definition of forceNoPBC (distance component)
• oneSiteTotalForce: see definition of oneSiteTotalForce (distance component)

### distanceDir: distance unit vector between two groups.

The distanceDir {...} block defines a distance unit vector component, which accepts the same keywords as the component distance: group1, group2, and forceNoPBC. It returns a 3-dimensional unit vector , with .

• group1: see definition of group1 (distance component)
• group2: analogous to group1
• forceNoPBC: see definition of forceNoPBC (distance component)
• oneSiteTotalForce: see definition of oneSiteTotalForce (distance component)

### distanceInv: mean distance between two groups of atoms.

The distanceInv {...} block defines a generalized mean distance between two groups of atoms 1 and 2, weighted with exponent :

 (13.2)

where is the distance between atoms and in groups 1 and 2 respectively, and is an even integer.

• group1: see definition of group1 (distance component)
• group2: analogous to group1
• oneSiteTotalForce: see definition of oneSiteTotalForce (distance component)
• exponent Exponent in equation 13.2
Context: distanceInv
Acceptable values: positive even integer
Default value: 6
Description: Defines the exponent to which the individual distances are elevated before averaging. The default value of 6 is useful for example to applying restraints based on NOE-measured distances.
This component returns a number in Å, ranging from 0 to the largest possible distance within the chosen boundary conditions.

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