.. _bad:
Bonds/distances, angles and dihedrals
-------------------------------------
| :ref:`gmx distance `, :ref:`gmx angle `,
:ref:`gmx gangle `
| To monitor specific *bonds* in your modules, or more generally
distances between points, the program
:ref:`gmx distance ` can calculate distances as a
function of time, as well as the distribution of the distance. With a
traditional index file, the groups should consist of pairs of atom
numbers, for example:
::
[ bonds_1 ]
1 2
3 4
9 10
[ bonds_2 ]
12 13
Selections are also supported, with first two positions defining the
first distance, second pair of positions defining the second distance
and so on. You can calculate the distances between CA and CB atoms in
all your residues (assuming that every residue either has both atoms, or
neither) using a selection such as:
::
name CA CB
The selections also allow more generic distances to be computed. For
example, to compute the distances between centers of mass of two
residues, you can use:
::
com of resname AAA plus com of resname BBB
The program :ref:`gmx angle `
calculates the distribution of *angles* and *dihedrals* in time. It also
gives the average angle or dihedral. The index file consists of triplets
or quadruples of atom numbers:
::
[ angles ]
1 2 3
2 3 4
3 4 5
[ dihedrals ]
1 2 3 4
2 3 5 5
For the dihedral angles you can use either the “biochemical convention”
(:math:`\phi = 0 \equiv cis`) or “polymer convention”
(:math:`\phi = 0 \equiv trans`), see
:numref:`Fig. %s `.
.. _fig-dihdef:
.. figure:: plots/dih-def.*
:width: 5.00000cm
Dihedral conventions: A. “Biochemical convention”. B. “Polymer
convention”.
The program :ref:`gmx gangle `
provides a selection-enabled version to compute angles. This tool can
also compute angles and dihedrals, but does not support all the options
of :ref:`gmx angle `, such as autocorrelation or other time
series analyses. In addition, it supports angles between two vectors, a
vector and a plane, two planes (defined by 2 or 3 points, respectively),
a vector/plane and the :math:`z` axis, or a vector/plane and the normal
of a sphere (determined by a single position). Also the angle between a
vector/plane compared to its position in the first frame is supported.
For planes, :ref:`gmx gangle `
uses the normal vector perpendicular to the plane. See
:numref:`Fig. %s ` A, B, C) for the definitions.
.. _fig-sgangle:
.. figure:: plots/sgangle.*
:width: 10.00000cm
Angle options of :ref:`gmx gangle `: A. Angle between two
vectors. B. Angle between two planes. C. Angle between a vector and the
:math:`z` axis. D. Angle between a vector and the normal of a sphere.
Also other combinations are supported: planes and vectors can be used
interchangeably.