Distances

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

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

List of keywords (see also for additional options):

• group1 $\langle\,$ First group of atoms$\,\rangle$
  Context: distance
  Acceptable values: Block group1 {...}
  Description: First group of atoms.

• group2: analogous to group1

• forceNoPBC $\langle\,$ Calculate absolute rather than minimum-image distance?$\,\rangle$
  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 $\langle\,$ Measure total force on group 1 only?$\,\rangle$
  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.

List of keywords (see also for additional options):

• main $\langle\,$ Main group of atoms$\,\rangle$
  Context: distanceZ
  Acceptable values: Block main {...}
  Description: Group of atoms whose position ${\mbox{\boldmath {$r$}}}$ is measured.

• ref $\langle\,$ Reference group of atoms$\,\rangle$
  Context: distanceZ
  Acceptable values: Block ref {...}
  Description: Reference group of atoms. The position of its center of mass is noted ${\mbox{\boldmath {$r$}}}_1$ below.

• ref2 $\langle\,$ Secondary reference group$\,\rangle$
  Context: distanceZ
  Acceptable values: Block ref2 {...}
  Default value: none
  Description: Optional group of reference atoms, whose position ${\mbox{\boldmath {$r$}}}_2$ can be used to define a dynamic projection axis: ${\mbox{\boldmath {$e$}}}=(\Vert {\mbox{\boldmath {$r$}}}_2 - {\mbox{\boldmath ... ...}_1\Vert)^{-1} \times ({\mbox{\boldmath {$r$}}}_2 - {\mbox{\boldmath {$r$}}}_1)$ . In this case, the origin is ${\mbox{\boldmath {$r$}}}_m = 1/2 ({\mbox{\boldmath {$r$}}}_1+{\mbox{\boldmath {$r$}}}_2)$ , and the value of the component is ${\mbox{\boldmath {$e$}}} \cdot ({\mbox{\boldmath {$r$}}}-{\mbox{\boldmath {$r$}}}_m)$ .

• axis $\langle\,$ Projection axis (Å)$\,\rangle$
  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 ${\mbox{\boldmath {$e$}}}$ for the distance vector ${\mbox{\boldmath {$r$}}} - {\mbox{\boldmath {$r$}}}_1$ joining the centers of groups ref and main. The value of the component is then ${\mbox{\boldmath {$e$}}} \cdot ({\mbox{\boldmath {$r$}}}-{\mbox{\boldmath {$r$}}}_1)$ . 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 $z$ axis is used in a simulation with periodic boundaries, the returned value ranges between $-b_{z}/2$ and $b_{z}/2$ , where $b_{z}$ is the box length along $z$ (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).

List of keywords (see also for additional options):

• 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.

List of keywords (see also for additional options):

• 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 $\mathbf{d} = (d_{x}, d_{y}, d_{z})$ , with $\vert\mathbf{d}\vert = 1$ .

List of keywords (see also for additional options):

• 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 $1/n$ :

$$d_{\mathrm{1,2}}^{[n]} \; = \; \left(\frac{1}{N_{\mathrm{1}}N_{\m... ...}\sum_{i,j} \left(\frac{1}{\Vert\mathbf{d}^{ij}\Vert}\right)^{n} \right)^{-1/n}$$ (13.2)

where $\Vert\mathbf{d}^{ij}\Vert$ is the distance between atoms $i$ and $j$ in groups 1 and 2 respectively, and $n$ is an even integer.

List of keywords (see also for additional options):

• group1: see definition of group1 (distance component)
• group2: analogous to group1
• oneSiteTotalForce: see definition of oneSiteTotalForce (distance component)
• exponent $\langle\,$ Exponent $n$ in equation 13.2$\,\rangle$
  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.