Generate a pair list with buffering. The buffer size is
automatically set based on :mdp:`verlet-buffer-tolerance`,
unless this is set to -1, in which case :mdp:`rlist` will be
- used. This option has an explicit, exact cut-off at :mdp:`rvdw`
- equal to :mdp:`rcoulomb`, unless PME or Ewald is used, in which
- 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-value:`cutoff-scheme=Verlet` scheme, but :ref:`gmx grompp`
- checks for this. Native GPU acceleration is only supported with
- :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-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.
+ used.
.. mdp-value:: group
- Generate a pair list for groups of atoms. These groups
- correspond to the charge groups in the topology. This was the
- only cut-off treatment scheme before version 4.6, and is
- **deprecated since 5.1**. There is no explicit buffering of
- the pair list. This enables efficient force calculations for
- water, but energy is only conserved when a buffer is explicitly
- added.
+ Generate a pair list for groups of atoms, corresponding
+ to the charge groups in the topology. This option is no longer
+ supported.
.. mdp:: nstlist
.. mdp-value:: >0
- Frequency to update the neighbor list. When this is 0, the
- neighbor list is made only once. With energy minimization the
- pair list will be updated for every energy evaluation when
- :mdp:`nstlist` is greater than 0. With :mdp-value:`cutoff-scheme=Verlet` and
+ Frequency to update the neighbor list. When dynamics 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-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.
+ the best performance.
.. mdp-value:: 0
The neighbor list is only constructed once and never
updated. This is mainly useful for vacuum simulations in which
- all particles see each other.
+ all particles see each other. But vacuum simulations are
+ (temporarily) not supported.
.. mdp-value:: <0
(0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
- Useful only with the :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`. This sets
+ Used when performing a simulation with dynamics. 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
:mdp:`epsilon-rf`. The dielectric constant can be set to
infinity by setting :mdp:`epsilon-rf` =0.
- .. mdp-value:: Reaction-Field-zero
-
- In |Gromacs|, normal reaction-field electrostatics with
- :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
- cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
- :mdp:`rcoulomb` to accommodate 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
- 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-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.
-
- .. mdp-value:: Encad-Shift
-
- The Coulomb potential is decreased over the whole range, using
- the definition from the Encad simulation package.
-
- .. mdp-value:: Switch
-
- Analogous to :mdp-value:`vdwtype=Switch` for
- :mdp:`vdwtype`. Switching the Coulomb potential can lead to
- serious artifacts, advice: use :mdp-value:`coulombtype=Reaction-Field-zero`
- instead.
-
.. mdp-value:: User
+ Currently unsupported.
:ref:`gmx mdrun` will now expect to find a file ``table.xvg``
with user-defined potential functions for repulsion, dispersion
and Coulomb. When pair interactions are present, :ref:`gmx
.. mdp-value:: PME-Switch
+ Currently unsupported.
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-value:`cutoff-scheme=Verlet`
- will be more efficient).
+ :mdp:`rlist`.
.. mdp-value:: PME-User
+ Currently unsupported.
A combination of PME and user tables (see
above). :mdp:`rcoulomb` is allowed to be smaller than
:mdp:`rlist`. The PME mesh contribution is subtracted from the
.. mdp-value:: PME-User-Switch
+ Currently unsupported.
A combination of PME-User and a switching function (see
above). The switching function is applied to final
particle-particle interaction, *i.e.* both to the user supplied
:mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
The LJ (not Buckingham) potential is decreased over the whole range and
the forces decay smoothly to zero between :mdp:`rvdw-switch` and
- :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
- be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
- size of charge groups and diffusion between neighbor list
- updates.
+ :mdp:`rvdw`.
.. mdp-value:: Switch
potential and force functions are continuously smooth, but be
aware that all switch functions will give rise to a bulge
(increase) in the force (since we are switching the
- potential). The neighbor search cut-off :mdp:`rlist` should be
- 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
- size of charge groups and diffusion between neighbor list
- updates.
-
- .. mdp-value:: Encad-Shift
-
- The LJ (not Buckingham) potential is decreased over the whole
- range, using the definition from the Encad simulation package.
+ potential).
.. mdp-value:: User
+ Currently unsupported.
See user for :mdp:`coulombtype`. The function value at zero is
not important. When you want to use LJ correction, make sure
that :mdp:`rvdw` corresponds to the cut-off in the user-defined
(1) [nm]
Extension of the non-bonded potential lookup tables beyond the
- largest cut-off distance. The value should be large enough to
- account for charge group sizes and the diffusion between
- neighbor-list updates. Without user defined potential the same
- table length is used for the lookup tables for the 1-4
- interactions, which are always tabulated irrespective of the use of
- tables for the non-bonded interactions. The value of
- :mdp:`table-extension` in no way affects the values of
- :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
+ largest cut-off distance. With actual non-bonded interactions
+ the tables are never accessed beyond the cut-off. But a longer
+ table length might be needed for the 1-4 interactions, which
+ are always tabulated irrespective of the use of tables for
+ the non-bonded interactions.
.. mdp:: energygrp-table
+ Currently unsupported.
When user tables are used for electrostatics and/or VdW, here one
can give pairs of energy groups for which seperate user tables
should be used. The two energy groups will be appended to the table
SHAKE is slightly slower and less stable than LINCS, but does
work with angle constraints. The relative tolerance is set with
:mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
- does not support constraints between atoms on different nodes,
- thus it can not be used with domain decompositon when inter
- charge-group constraints are present. SHAKE can not be used with
- energy minimization.
+ does not support constraints between atoms on different
+ decomposition domains, so it can only be used with domain
+ decomposition when so-called update-groups are used, which is
+ usally the case when only bonds involving hydrogens are
+ constrained. SHAKE can not be used with energy minimization.
.. mdp:: continuation
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff