molecule. When :mdp:`nstlist` is larger than one,
:mdp:`nstlist` insertions are performed in a sphere with radius
:mdp:`rtpi` around a the same random location using the same
- neighborlist. Since neighborlist construction is expensive,
+ pair list. Since pair list construction is expensive,
one can perform several extra insertions with the same list
almost for free. The random seed is set with
:mdp:`ld-seed`. The temperature for the Boltzmann weighting is
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 in |gmx-version|**. There is no explicit buffering of
+ **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.
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
+ pair list will be updated for every energy evaluation when
: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
.. mdp-value:: Cut-off
- Plain cut-off with neighborlist radius :mdp:`rlist` and
+ Plain cut-off with pair list radius :mdp:`rlist` and
Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
:mdp:`rcoulomb`.
Use an unmodified Coulomb potential. With the group scheme this
means no exact cut-off is used, energies and forces are
- calculated for all pairs in the neighborlist.
+ calculated for all pairs in the pair list.
.. mdp:: rcoulomb-switch
.. mdp-value:: Cut-off
- Twin range cut-offs with neighbor list cut-off :mdp:`rlist` and
- VdW cut-off :mdp:`rvdw`, where :mdp:`rvdw` >= :mdp:`rlist`.
+ Plain cut-off with pair list radius :mdp:`rlist` and VdW
+ cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
.. mdp-value:: PME
Use an unmodified Van der Waals potential. With the group scheme
this means no exact cut-off is used, energies and forces are
- calculated for all pairs in the neighborlist.
+ calculated for all pairs in the pair list.
.. mdp-value:: Force-switch
.. mdp:: constraints
+ Controls which bonds in the topology will be converted to rigid
+ holonomic constraints. Note that typical rigid water models do not
+ have bonds, but rather a specialized ``[settles]`` directive, so
+ are not affected by this keyword.
+
.. mdp-value:: none
- No constraints except for those defined explicitly in the
- topology, *i.e.* bonds are represented by a harmonic (or other)
- potential or a Morse potential (depending on the setting of
- :mdp:`morse`) and angles by a harmonic (or other) potential.
+ No bonds converted to constraints.
.. mdp-value:: h-bonds
.. mdp-value:: h-angles
- Convert all bonds and additionally the angles that involve
- H-atoms to bond-constraints.
+ Convert all bonds to constraints and convert the angles that
+ involve H-atoms to bond-constraints.
.. mdp-value:: all-angles
- Convert all bonds and angles to bond-constraints.
+ Convert all bonds to constraints and all angles to bond-constraints.
.. mdp:: constraint-algorithm
+ Chooses which solver satisfies any non-SETTLE holonomic
+ constraints.
+
.. mdp-value:: LINCS
LINear Constraint Solver. With domain decomposition the parallel
.. mdp:: continuation
- This option was formerly known as unconstrained-start.
+ This option was formerly known as ``unconstrained-start``.
.. mdp-value:: no
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