case :mdp:`rcoulomb` > :mdp:`rvdw` is allowed. Currently only
cut-off, reaction-field, PME or Ewald electrostatics and plain
LJ are supported. Some :ref:`gmx mdrun` functionality is not yet
- supported with the :mdp:`Verlet` scheme, but :ref:`gmx grompp`
+ supported with the :mdp-value:`cutoff-scheme=Verlet` scheme, but :ref:`gmx grompp`
checks for this. Native GPU acceleration is only supported with
- :mdp:`Verlet`. With GPU-accelerated PME or with separate PME
+ :mdp-value:`cutoff-scheme=Verlet`. With GPU-accelerated PME or with separate PME
ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
balance by scaling :mdp:`rcoulomb` and the grid spacing. This
- can be turned off with ``mdrun -notunepme``. :mdp:`Verlet` is
- faster than :mdp:`group` when there is no water, or if
- :mdp:`group` would use a pair-list buffer to conserve energy.
+ can be turned off with ``mdrun -notunepme``. :mdp-value:`cutoff-scheme=Verlet` is
+ faster than :mdp-value:`cutoff-scheme=group` when there is no water, or if
+ :mdp-value:`cutoff-scheme=group` would use a pair-list buffer to conserve energy.
.. mdp-value:: group
Frequency to update the neighbor list. When this is 0, the
neighbor list is made only once. With energy minimization the
neighborlist will be updated for every energy evaluation when
- :mdp:`nstlist` is greater than 0. With :mdp:`Verlet` and
+ :mdp:`nstlist` is greater than 0. With :mdp-value:`cutoff-scheme=Verlet` and
:mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
a minimum value and :ref:`gmx mdrun` might increase it, unless
it is set to 1. With parallel simulations and/or non-bonded
force calculation on the GPU, a value of 20 or 40 often gives
- the best performance. With :mdp:`group` and non-exact
+ the best performance. With :mdp-value:`cutoff-scheme=group` and non-exact
cut-off's, :mdp:`nstlist` will affect the accuracy of your
simulation and it can not be chosen freely.
.. mdp-value:: simple
Check every atom in the box when constructing a new neighbor
- list every :mdp:`nstlist` steps (only with :mdp:`group`
+ list every :mdp:`nstlist` steps (only with :mdp-value:`cutoff-scheme=group`
cut-off scheme).
.. mdp:: pbc
(0.005) \[kJ/mol/ps\]
- Useful only with the :mdp:`Verlet` :mdp:`cutoff-scheme`. This sets
+ Useful only with the :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`. This sets
the maximum allowed error for pair interactions per particle caused
by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
:mdp:`nstlist` and the Verlet buffer size are fixed (for
(1) \[nm\]
Cut-off distance for the short-range neighbor list. With the
- :mdp:`Verlet` :mdp:`cutoff-scheme`, this is by default set by the
+ :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`, this is by default set by the
:mdp:`verlet-buffer-tolerance` option and the value of
:mdp:`rlist` is ignored.
.. mdp-value:: Reaction-Field-zero
In |Gromacs|, normal reaction-field electrostatics with
- :mdp:`cutoff-scheme` = :mdp:`group` leads to bad energy
- conservation. :mdp:`Reaction-Field-zero` solves this by making
+ :mdp:`cutoff-scheme` = :mdp-value:`cutoff-scheme=group` leads to bad energy
+ conservation. :mdp-value:`coulombtype=Reaction-Field-zero` solves this by making
the potential zero beyond the cut-off. It can only be used with
an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
only for that value the force vanishes at the
:mdp:`rcoulomb` to accommodate for the size of charge groups
and diffusion between neighbor list updates. This, and the fact
that table lookups are used instead of analytical functions make
- :mdp:`Reaction-Field-zero` computationally more expensive than
+ :mdp-value:`coulombtype=Reaction-Field-zero` computationally more expensive than
normal reaction-field.
.. mdp-value:: Shift
Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
- might want to use :mdp:`Reaction-Field-zero` instead, which has
+ might want to use :mdp-value:`coulombtype=Reaction-Field-zero` instead, which has
a similar potential shape, but has a physical interpretation and
has better energies due to the exclusion correction terms.
Analogous to :mdp-value:`vdwtype=Switch` for
:mdp:`vdwtype`. Switching the Coulomb potential can lead to
- serious artifacts, advice: use :mdp:`Reaction-Field-zero`
+ serious artifacts, advice: use :mdp-value:`coulombtype=Reaction-Field-zero`
instead.
.. mdp-value:: User
A combination of PME and a switch function for the direct-space
part (see above). :mdp:`rcoulomb` is allowed to be smaller than
:mdp:`rlist`. This is mainly useful constant energy simulations
- (note that using PME with :mdp:`cutoff-scheme` = :mdp:`Verlet`
+ (note that using PME with :mdp:`cutoff-scheme` = :mdp-value:`cutoff-scheme=Verlet`
will be more efficient).
.. mdp-value:: PME-User
.. mdp-value:: MTTK
Martyna-Tuckerman-Tobias-Klein implementation, only useable with
- :mdp-value:`md-vv` or :mdp-value:`md-vv-avek`, very similar to
+ :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
Parrinello-Rahman. As for Nose-Hoover temperature coupling the
time constant :mdp:`tau-p` is the period of pressure
fluctuations at equilibrium. This is probably a better method
(1.5) \[nm\]
the radius of the cylinder for
- :mdp:`pull-coord1-geometry` = :mdp-value:`cylinder`
+ :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=cylinder`
.. mdp:: pull-constr-tol
.. mdp-value:: direction-periodic
- As :mdp-value:`direction`, but allows the distance to be larger
+ As :mdp-value:`pull-coord1-geometry=direction`, but allows the distance to be larger
than half the box size. With this geometry the box should not be
dynamic (*e.g.* no pressure scaling) in the pull dimensions and
the pull force is not added to virial.
.. mdp-value:: direction-relative
- As :mdp-value:`direction`, but the pull vector is the vector
+ As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
that points from the COM of a third to the COM of a fourth pull
group. This means that 4 groups need to be supplied in
:mdp:`pull-coord1-groups`. Note that the pull force will give
.. mdp-value:: angle-axis
- As :mdp-value:`angle` but the second vector is given by :mdp:`pull-coord1-vec`.
+ As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
Thus, only the two groups that define the first vector need to be given.
.. mdp-value:: dihedral
(Y Y Y)
Selects the dimensions that this pull coordinate acts on and that
are printed to the output files when
- :mdp:`pull-print-components` = :mdp-value:`yes`. With
- :mdp:`pull-coord1-geometry` = :mdp-value:`distance`, only Cartesian
+ :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
+ :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
components set to Y contribute to the distance. Thus setting this
to Y Y N results in a distance in the x/y plane. With other
geometries all dimensions with non-zero entries in
.. mdp-value:: yes
- Apply the rotation potential specified by :mdp:`rot-type` to the group of atoms given
- under the :mdp:`rot-group` option.
+ Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
+ under the :mdp:`rot-group0` option.
.. mdp:: rot-ngroups
Electric fields
^^^^^^^^^^^^^^^
-.. mdp:: E-x ; E-y ; E-z
+.. mdp:: E-x; E-y; E-z
If you want to use an electric field in a direction, enter 3
numbers after the appropriate E-direction, the first number: the
E(t) = E0 exp ( -(t-t0)^2/(2 sigma^2) ) cos(omega (t-t0))
For example, the four parameters for direction x are set in the
- three fields of :mdp:`E-x` and :mdp:`E-xt` like
+ three fields of :mdp:`E-x; E-y; E-z` and :mdp:`E-xt; E-yt; E-zt` like
E-x = 1 E0 0
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff