.. mdp-value:: 3dc
The reciprocal sum is still performed in 3D, but a force and
- potential correction applied in the `z` dimension to produce a
+ potential correction applied in the ``z`` dimension to produce a
pseudo-2D summation. If your system has a slab geometry in the
- `x-y` plane you can try to increase the `z`-dimension of the box
+ ``x-y`` plane you can try to increase the ``z``-dimension of the box
(a box height of 3 times the slab height is usually ok) and use
this option.
.. mdp-value:: surface-tension
Surface tension coupling for surfaces parallel to the
- xy-plane. Uses normal pressure coupling for the `z`-direction,
- while the surface tension is coupled to the `x/y` dimensions of
+ xy-plane. Uses normal pressure coupling for the ``z``-direction,
+ while the surface tension is coupled to the ``x/y`` dimensions of
the box. The first :mdp:`ref-p` value is the reference surface
tension times the number of surfaces ``bar nm``, the second
- value is the reference `z`-pressure ``bar``. The two
+ value is the reference ``z``-pressure ``bar``. The two
:mdp:`compressibility` values are the compressibility in the
- `x/y` and `z` direction respectively. The value for the
- `z`-compressibility should be reasonably accurate since it
+ ``x/y`` and ``z`` direction respectively. The value for the
+ ``z``-compressibility should be reasonably accurate since it
influences the convergence of the surface-tension, it can also
be set to zero to have a box with constant height.
(1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
force constant for distance restraints, which is multiplied by a
- (possibly) different factor for each restraint given in the `fac`
+ (possibly) different factor for each restraint given in the ``fac``
column of the interaction in the topology file.
.. mdp:: disre-tau
.. mdp:: freezedim
dimensions for which groups in :mdp:`freezegrps` should be frozen,
- specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
- N N N N`` means that particles in the first group can move only in
+ specify ``Y`` or ``N`` for X, Y and Z and for each group (*e.g.*
+ ``Y Y N N N N`` means that particles in the first group can move only in
Z direction. The particles in the second group can move in any
direction).
.. mdp:: QMcharge
(0) [integer]
- The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
+ The total charge in ``e`` of the :mdp:`QMMM-grps`. In case there are
more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
layer needs to be specified separately.