From: Paul Bauer Date: Wed, 1 Nov 2017 11:44:51 +0000 (+0100) Subject: Fixing missing references in web documentation X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=50b2dd842b0a69080d25f7f6d9aced0c20fc7e11;p=alexxy%2Fgromacs.git Fixing missing references in web documentation Change-Id: Ifca209c15f4cec3fed24e2070df8fa85320d02dd --- diff --git a/docs/user-guide/environment-variables.rst b/docs/user-guide/environment-variables.rst index 76fd587706..217629c61c 100644 --- a/docs/user-guide/environment-variables.rst +++ b/docs/user-guide/environment-variables.rst @@ -363,7 +363,7 @@ Performance and Run Control ``GMX_NSTLIST_DYNAMICPRUNING`` overrides the dynamic pair-list pruning interval chosen heuristically by mdrun. Values should be between the pruning frequency value - (1 for CPU and 2 for GPU) and :mdp:`nstlist - 1`. + (1 for CPU and 2 for GPU) and :mdp:`nstlist` ``- 1``. ``GMX_USE_TREEREDUCE`` use tree reduction for nbnxn force reduction. Potentially faster for large number of diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst index 8666f64d34..2cf52f786b 100644 --- a/docs/user-guide/mdp-options.rst +++ b/docs/user-guide/mdp-options.rst @@ -422,14 +422,14 @@ Neighbor searching 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 @@ -450,12 +450,12 @@ Neighbor searching 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. @@ -481,7 +481,7 @@ Neighbor searching .. 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 @@ -522,7 +522,7 @@ Neighbor searching (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 @@ -553,7 +553,7 @@ Neighbor searching (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. @@ -624,8 +624,8 @@ Electrostatics .. 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 @@ -633,13 +633,13 @@ Electrostatics :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. @@ -652,7 +652,7 @@ Electrostatics 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 @@ -683,7 +683,7 @@ Electrostatics 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 @@ -1115,7 +1115,7 @@ Pressure coupling .. 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 @@ -1546,7 +1546,7 @@ applicable pulling coordinate. (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 @@ -1693,14 +1693,14 @@ applicable pulling coordinate. .. 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 @@ -1739,7 +1739,7 @@ applicable pulling coordinate. .. 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 @@ -1767,8 +1767,8 @@ applicable pulling coordinate. (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 @@ -1841,8 +1841,8 @@ that can be used to achieve such a rotation. .. 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 @@ -2689,7 +2689,7 @@ Non-equilibrium MD 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 @@ -2706,7 +2706,7 @@ Electric fields 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 diff --git a/docs/user-guide/mdrun-performance.rst b/docs/user-guide/mdrun-performance.rst index f6f254b700..2d7b85ad57 100644 --- a/docs/user-guide/mdrun-performance.rst +++ b/docs/user-guide/mdrun-performance.rst @@ -803,8 +803,8 @@ Run setup ^^^^^^^^^ * For an approximately spherical solute, use a rhombic dodecahedron unit cell. -* When using a time-step of 2 fs, use :mdp:`cutoff-scheme` = :mdp:`h-bonds` - (and not :mdp:`all-bonds`), since this is faster, especially with GPUs, +* When using a time-step of 2 fs, use :mdp:`cutoff-scheme` = :mdp-value:`constraints=h-bonds` + (and not :mdp-value:`constraints=all-bonds`), since this is faster, especially with GPUs, and most force fields have been parametrized with only bonds involving hydrogens constrained. * You can increase the time-step to 4 or 5 fs when using virtual interaction