From: Kevin Boyd Date: Fri, 25 May 2018 01:37:27 +0000 (-0400) Subject: Cosmetic fixes to mdp documentation X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=f2df4657f25bca768493117b922d6ea0e12ed6c8;p=alexxy%2Fgromacs.git Cosmetic fixes to mdp documentation Mostly grammar/tense/linking Added specific mentions of .trr and .xtc file extensions in output control Properly formatted superscripts, removed unneccessary escape characters in units Change-Id: Ia359ffae1c54075d2fcc36c7b7b81acef779f608 --- diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst index 19d5b944ab..cb93e10ad5 100644 --- a/docs/user-guide/mdp-options.rst +++ b/docs/user-guide/mdp-options.rst @@ -182,13 +182,13 @@ Run control .. mdp:: tinit - (0) \[ps\] + (0) [ps] starting time for your run (only makes sense for time-based integrators) .. mdp:: dt - (0.001) \[ps\] + (0.001) [ps] time step for integration (only makes sense for time-based integrators) @@ -201,7 +201,7 @@ Run control .. mdp:: init-step (0) - The starting step. The time at an step i in a run is + The starting step. The time at step i in a run is calculated as: t = :mdp:`tinit` + :mdp:`dt` * (:mdp:`init-step` + i). The free-energy lambda is calculated as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` * @@ -228,15 +228,14 @@ Run control .. mdp-value:: Angular - Remove center of mass translational and rotational velocity around - the center of mass + Remove center of mass translational and rotational velocity .. mdp-value:: Linear-acceleration-correction Remove center of mass translational velocity. Correct the center of mass position assuming linear acceleration over :mdp:`nstcomm` steps. This is useful for cases where an acceleration is expected on the - center of mass which is nearly constant over mdp:`nstcomm` steps. + center of mass which is nearly constant over :mdp:`nstcomm` steps. This can occur for example when pulling on a group using an absolute reference. @@ -246,7 +245,7 @@ Run control .. mdp:: nstcomm - (100) \[steps\] + (100) [steps] frequency for center of mass motion removal .. mdp:: comm-grps @@ -260,14 +259,14 @@ Langevin dynamics .. mdp:: bd-fric - (0) \[amu ps-1\] + (0) [amu ps\ :sup:`-1`] Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0, the friction coefficient for each particle is calculated as mass/ :mdp:`tau-t`. .. mdp:: ld-seed - (-1) \[integer\] + (-1) [integer] used to initialize random generator for thermal noise for stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1, a pseudo random seed is used. When running BD or SD on multiple @@ -280,18 +279,18 @@ Energy minimization .. mdp:: emtol - (10.0) \[kJ mol-1 nm-1\] + (10.0) [kJ mol\ :sup:`-1` nm\ :sup:`-1`] the minimization is converged when the maximum force is smaller than this value .. mdp:: emstep - (0.01) \[nm\] + (0.01) [nm] initial step-size .. mdp:: nstcgsteep - (1000) \[steps\] + (1000) [steps] frequency of performing 1 steepest descent step while doing conjugate gradient energy minimization. @@ -321,7 +320,7 @@ value should be 1.0 at most. .. mdp:: fcstep - (0) \[ps^2\] + (0) [ps\ :sup:`2`] the step size for optimizing the flexible constraints. Should be chosen as mu/(d2V/dq2) where mu is the reduced mass of two particles in a flexible constraint and d2V/dq2 is the second @@ -336,7 +335,7 @@ Test particle insertion .. mdp:: rtpi - (0.05) \[nm\] + (0.05) [nm] the test particle insertion radius, see integrators :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic` @@ -346,25 +345,25 @@ Output control .. mdp:: nstxout - (0) \[steps\] - number of steps that elapse between writing coordinates to output - trajectory file, the last coordinates are always written + (0) [steps] + number of steps that elapse between writing coordinates to the output + trajectory file (:ref:`trr`), the last coordinates are always written .. mdp:: nstvout - (0) \[steps\] - number of steps that elapse between writing velocities to output - trajectory, the last velocities are always written + (0) [steps] + number of steps that elapse between writing velocities to the output + trajectory file (:ref:`trr`), the last velocities are always written .. mdp:: nstfout - (0) \[steps\] - number of steps that elapse between writing forces to output - trajectory. + (0) [steps] + number of steps that elapse between writing forces to the output + trajectory file (:ref:`trr`), the last forces are always written. .. mdp:: nstlog - (1000) \[steps\] + (1000) [steps] number of steps that elapse between writing energies to the log file, the last energies are always written @@ -379,8 +378,8 @@ Output control .. mdp:: nstenergy - (1000) \[steps\] - number of steps that else between writing energies to energy file, + (1000) [steps] + number of steps that elapse between writing energies to energy file, the last energies are always written, should be a multiple of :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations over all MD steps modulo :mdp:`nstcalcenergy` are stored in the @@ -389,13 +388,13 @@ Output control .. mdp:: nstxout-compressed - (0) \[steps\] + (0) [steps] number of steps that elapse between writing position coordinates - using lossy compression + using lossy compression (:ref:`xtc` file) .. mdp:: compressed-x-precision - (1000) \[real\] + (1000) [real] precision with which to write to the compressed trajectory file .. mdp:: compressed-x-grps @@ -445,7 +444,7 @@ Neighbor searching .. mdp:: nstlist - \(10) \[steps\] + (10) [steps] .. mdp-value:: >0 @@ -497,12 +496,12 @@ Neighbor searching Use no periodic boundary conditions, ignore the box. To simulate without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For best performance without cut-offs on a single MPI rank, set - :mdp:`nstlist` to zero and :mdp:`ns-type` =simple. + :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`. .. mdp-value:: xy Use periodic boundary conditions in x and y directions - only. This works only with :mdp:`ns-type` =grid and can be used + only. This works only with :mdp-value:`ns-type=grid` and can be used in combination with walls_. Without walls or with only one wall the system size is infinite in the z direction. Therefore pressure coupling or Ewald summation methods can not be @@ -522,7 +521,7 @@ Neighbor searching .. mdp:: verlet-buffer-tolerance - (0.005) \[kJ/mol/ps\] + (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`] Useful only with the :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`. This sets the maximum allowed error for pair interactions per particle caused @@ -553,7 +552,7 @@ Neighbor searching .. mdp:: rlist - (1) \[nm\] + (1) [nm] Cut-off distance for the short-range neighbor list. With 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 @@ -580,7 +579,7 @@ Electrostatics :mdp:`fourierspacing`. The relative accuracy of direct/reciprocal space is controlled by :mdp:`ewald-rtol`. - NOTE: Ewald scales as O(N^3/2) and is thus extremely slow for + NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for large systems. It is included mainly for reference - in most cases PME will perform much better. @@ -592,7 +591,7 @@ Electrostatics :mdp:`fourierspacing` and the interpolation order with :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic interpolation the electrostatic forces have an accuracy of - 2-3*10^-4. Since the error from the vdw-cutoff is larger than + 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than this you might try 0.15 nm. When running in parallel the interpolation parallelizes better than the FFT, so try decreasing grid dimensions while increasing interpolation. @@ -626,16 +625,16 @@ Electrostatics .. mdp-value:: Reaction-Field-zero In |Gromacs|, normal reaction-field electrostatics with - :mdp:`cutoff-scheme` = :mdp-value:`cutoff-scheme=group` leads to bad energy + :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 for the size of charge groups + :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 - :mdp-value:`coulombtype=Reaction-Field-zero` computationally more expensive than + reaction-field-zero computationally more expensive than normal reaction-field. .. mdp-value:: Shift @@ -685,7 +684,7 @@ 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-value:`cutoff-scheme=Verlet` + (note that using PME with :mdp-value:`cutoff-scheme=Verlet` will be more efficient). .. mdp-value:: PME-User @@ -725,13 +724,13 @@ Electrostatics .. mdp:: rcoulomb-switch - (0) \[nm\] + (0) [nm] where to start switching the Coulomb potential, only relevant when force or potential switching is used .. mdp:: rcoulomb - (1) \[nm\] + (1) [nm] distance for the Coulomb cut-off .. mdp:: epsilon-r @@ -769,26 +768,26 @@ Van der Waals .. mdp-value:: Shift - This functionality is deprecated and replaced by - :mdp:`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 + This functionality is deprecated and replaced by using + :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 for the + 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:: Switch - This functionality is deprecated and replaced by - :mdp:`vdw-modifier` = Potential-switch. The LJ (not Buckingham) - potential is normal out to :mdp:`rvdw-switch`, after which it - is switched off to reach zero at :mdp:`rvdw`. Both the + This functionality is deprecated and replaced by using + :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`. + The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after + which it is switched off to reach zero at :mdp:`rvdw`. Both the 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 for the + 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the size of charge groups and diffusion between neighbor list updates. @@ -844,14 +843,13 @@ Van der Waals .. mdp:: rvdw-switch - (0) \[nm\] - + (0) [nm] where to start switching the LJ force and possibly the potential, only relevant when force or potential switching is used .. mdp:: rvdw - (1) \[nm\] + (1) [nm] distance for the LJ or Buckingham cut-off .. mdp:: DispCorr @@ -874,7 +872,7 @@ Tables .. mdp:: table-extension - (1) \[nm\] + (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 @@ -903,7 +901,7 @@ Ewald .. mdp:: fourierspacing - (0.12) \[nm\] + (0.12) [nm] For ordinary Ewald, the ratio of the box dimensions and the spacing determines a lower bound for the number of wave vectors to use in each (signed) direction. For PME and P3M, that ratio determines a @@ -935,7 +933,7 @@ Ewald .. mdp:: ewald-rtol - (1e-5) + (10\ :sup:`-5`) The relative strength of the Ewald-shifted direct potential at :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this will give a more accurate direct sum, but then you need more wave @@ -943,7 +941,7 @@ Ewald .. mdp:: ewald-rtol-lj - (1e-3) + (10\ :sup:`-3`) When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used to control the relative strength of the dispersion potential at :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the @@ -1003,7 +1001,7 @@ Temperature coupling .. mdp-value:: berendsen - Temperature coupling with a Berendsen-thermostat to a bath with + Temperature coupling with a Berendsen thermostat to a bath with temperature :mdp:`ref-t`, with time constant :mdp:`tau-t`. Several groups can be coupled separately, these are specified in the :mdp:`tc-grps` field separated by spaces. @@ -1015,11 +1013,11 @@ Temperature coupling but in this case :mdp:`tau-t` controls the period of the temperature fluctuations at equilibrium, which is slightly different from a relaxation time. For NVT simulations the - conserved energy quantity is written to energy and log file. + conserved energy quantity is written to the energy and log files. .. mdp-value:: andersen - Temperature coupling by randomizing a fraction of the particles + Temperature coupling by randomizing a fraction of the particle velocities at each timestep. Reference temperature and coupling groups are selected as above. :mdp:`tau-t` is the average time between randomization of each molecule. Inhibits particle dynamics @@ -1029,8 +1027,8 @@ Temperature coupling .. mdp-value:: andersen-massive - Temperature coupling by randomizing all particles at infrequent - timesteps. Reference temperature and coupling groups are + Temperature coupling by randomizing velocities of all particles at + infrequent timesteps. Reference temperature and coupling groups are selected as above. :mdp:`tau-t` is the time between randomization of all molecules. Inhibits particle dynamics somewhat, but little or no ergodicity issues. Currently only @@ -1081,13 +1079,13 @@ Temperature coupling .. mdp:: tau-t - \[ps\] + [ps] time constant for coupling (one for each group in :mdp:`tc-grps`), -1 means no temperature coupling .. mdp:: ref-t - \[K\] + [K] reference temperature for coupling (one for each group in :mdp:`tc-grps`) @@ -1119,7 +1117,7 @@ Pressure coupling equilibrium. This is probably a better method when you want to apply pressure scaling during data collection, but beware that you can get very large oscillations if you are starting from a - different pressure. For simulations where the exact fluctation + different pressure. For simulations where the exact fluctations of the NPT ensemble are important, or if the pressure coupling time is very short it may not be appropriate, as the previous time step pressure is used in some steps of the |Gromacs| @@ -1191,20 +1189,20 @@ Pressure coupling .. mdp:: tau-p - (1) \[ps\] + (1) [ps] The time constant for pressure coupling (one value for all directions). .. mdp:: compressibility - \[bar^-1\] - The compressibility (NOTE: this is now really in bar^-1) For water at 1 - atm and 300 K the compressibility is 4.5e-5 bar^-1. The number of + [bar\ :sup:`-1`] + The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1 + atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of required values is implied by :mdp:`pcoupltype`. .. mdp:: ref-p - \[bar\] + [bar] The reference pressure for coupling. The number of required values is implied by :mdp:`pcoupltype`. @@ -1318,16 +1316,16 @@ Velocity generation Generate velocities in :ref:`gmx grompp` according to a Maxwell distribution at temperature :mdp:`gen-temp`, with random seed :mdp:`gen-seed`. This is only meaningful with - integrator :mdp-value:`integrator=md`. + :mdp-value:`integrator=md`. .. mdp:: gen-temp - (300) \[K\] + (300) [K] temperature for Maxwell distribution .. mdp:: gen-seed - (-1) \[integer\] + (-1) [integer] used to initialize random generator for random velocities, when :mdp:`gen-seed` is set to -1, a pseudo random seed is used. @@ -1438,7 +1436,7 @@ Bonds .. mdp:: lincs-warnangle - (30) \[deg\] + (30) [deg] maximum angle that a bond can rotate before LINCS will complain .. mdp:: morse @@ -1474,7 +1472,7 @@ Walls (0) When set to 1 there is a wall at ``z=0``, when set to 2 there is also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc` - ``=xy``. When set to 2 pressure coupling and Ewald summation can be + ``=xy``. When set to 2, pressure coupling and Ewald summation can be used (it is usually best to use semiisotropic pressure coupling with the ``x/y`` compressibility set to 0, as otherwise the surface area will change). Walls interact wit the rest of the system @@ -1514,7 +1512,7 @@ Walls .. mdp:: wall-r-linpot - (-1) \[nm\] + (-1) [nm] Below this distance from the wall the potential is continued linearly and thus the force is constant. Setting this option to a postive value is especially useful for equilibration when some @@ -1524,7 +1522,7 @@ Walls .. mdp:: wall-density - \[nm^-3/nm^-2\] + [nm\ :sup:`-3`] / [nm\ :sup:`-2`] the number density of the atoms for each wall for wall types 9-3 and 10-4 @@ -1541,11 +1539,12 @@ Walls COM pulling ^^^^^^^^^^^ -Note that where pulling coordinate are applicable, there can be more +Note that where pulling coordinates are applicable, there can be more than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp` variables will exist accordingly. Documentation references to things like :mdp:`pull-coord1-vec` should be understood to apply to to the -applicable pulling coordinate. +applicable pulling coordinate, eg. the second pull coordinate is described by +pull-coord2-vec, pull-coord2-k, and so on. .. mdp:: pull @@ -1562,13 +1561,12 @@ applicable pulling coordinate. .. mdp:: pull-cylinder-r - (1.5) \[nm\] - the radius of the cylinder for - :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=cylinder` + (1.5) [nm] + the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder` .. mdp:: pull-constr-tol - (1e-6) + (10\ :sup:`-6`) the relative constraint tolerance for constraint pulling .. mdp:: pull-print-com @@ -1816,27 +1814,31 @@ applicable pulling coordinate. .. mdp:: pull-coord1-init - (0.0) \[nm\] / \[deg\] - The reference distance at t=0. + (0.0) [nm] or [deg] + The reference distance or reference angle at t=0. .. mdp:: pull-coord1-rate - (0) \[nm/ps\] / \[deg/ps\] - The rate of change of the reference position. + (0) [nm/ps] or [deg/ps] + The rate of change of the reference position or reference angle. .. mdp:: pull-coord1-k - (0) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\] + (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or + [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`] The force constant. For umbrella pulling this is the harmonic force - constant in kJ mol-1 nm-2 (or kJ mol-1 rad-2 for angles). For constant force pulling this is the + constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2` + for angles). For constant force pulling this is the force constant of the linear potential, and thus the negative (!) - of the constant force in kJ mol-1 nm-1 (or kJ mol-1 rad-1 for angles). + of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1` + (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles). Note that for angles the force constant is expressed in terms of radians (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees). .. mdp:: pull-coord1-kB - (pull-k1) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\] + (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] + or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`] As :mdp:`pull-coord1-k`, but for state B. This is only used when :mdp:`free-energy` is turned on. The force constant is then (1 - lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`. @@ -1930,7 +1932,7 @@ AWH adaptive biasing .. mdp:: awh1-error-init - (10.0) \[kJ mol-1\] + (10.0) [kJ mol\ :sup:`-1`] Estimated initial average error of the PMF for this bias. This value together with the given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate. The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init` @@ -1979,7 +1981,7 @@ AWH adaptive biasing .. mdp-value:: constant The bias is tuned towards a constant (uniform) coordinate distribution - in the defined sampling interval (defined by \[:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`\]). + in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]). .. mdp-value:: cutoff @@ -2007,13 +2009,13 @@ AWH adaptive biasing .. mdp:: awh1-target-beta-scaling - [0] \[\] + (0) For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann` it is the unitless beta scaling factor taking values in (0,1). .. mdp:: awh1-target-cutoff - [0] \[kJ mol-1\] + (0) [kJ mol\ :sup:`-1`] For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0. .. mdp:: awh1-user-data @@ -2054,7 +2056,7 @@ AWH adaptive biasing .. mdp:: awh1-ndim - (1) \[integer\] + (1) [integer] Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate. The following options should be specified for each such dimension. Below only the options for dimension number 1 is shown. Options for other dimension indices are @@ -2074,13 +2076,13 @@ AWH adaptive biasing .. mdp:: awh1-dim1-force-constant - (0) \[kJ/mol/nm^2\] or \[kJ/mol/rad^2\] + (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] Force constant for the (convolved) umbrella potential(s) along this coordinate dimension. .. mdp:: awh1-dim1-start - (0.0) \[nm\]/\[rad\] + (0.0) [nm] or [rad] Start value of the sampling interval along this dimension. The range of allowed values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`). For periodic geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end` @@ -2088,17 +2090,17 @@ AWH adaptive biasing .. mdp:: awh1-dim1-end - (0.0) \[nm\]/\[rad\] + (0.0) [nm] or [rad] End value defining the sampling interval together with :mdp:`awh1-dim1-start`. .. mdp:: awh1-dim1-period - (0.0) \[nm\]/\[rad\] + (0.0) [nm] or [rad] The period of this reaction coordinate, use 0 when the coordinate is not periodic. .. mdp:: awh1-dim1-diffusion - (1e-5) \[nm^2/ps\]/\[rad^2/ps\] + (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps] Estimated diffusion constant for this coordinate dimension determining the initial biasing rate. This needs only be a rough estimate and should not critically affect the results unless it is set to something very low, leading to slow convergence, @@ -2107,7 +2109,7 @@ AWH adaptive biasing .. mdp:: awh1-dim1-cover-diameter - (0.0)) \[nm\]/\[rad\] + (0.0) [nm] or [rad] Diameter that needs to be sampled by a single simulation around a coordinate value before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`). A value > 0 ensures that for each covering there is a continuous transition of this diameter @@ -2167,23 +2169,23 @@ that can be used to achieve such a rotation. .. mdp:: rot-pivot0 - (0.0 0.0 0.0) - Pivot point (nm) for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``. + (0.0 0.0 0.0) [nm] + Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``. .. mdp:: rot-rate0 - (0) - Reference rotation rate (degree/ps) of group 0. + (0) [degree ps\ :sup:`-1`] + Reference rotation rate of group 0. .. mdp:: rot-k0 - (0) - Force constant (kJ/(mol*nm^2)) for group 0. + (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] + Force constant for group 0. .. mdp:: rot-slab-dist0 - (1.5) - Slab distance (nm), if a flexible axis rotation type was chosen. + (1.5) [nm] + Slab distance, if a flexible axis rotation type was chosen. .. mdp:: rot-min-gauss0 @@ -2193,8 +2195,8 @@ that can be used to achieve such a rotation. .. mdp:: rot-eps0 - (0.0001) - Value of additive constant epsilon' (nm^2) for ``rm2*`` and ``flex2*`` potentials. + (0.0001) [nm\ :sup:`2`] + Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials. .. mdp:: rot-fit-method0 @@ -2277,20 +2279,20 @@ NMR refinement .. mdp:: disre-fc - (1000) \[kJ mol-1 nm-2\] + (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` column of the interaction in the topology file. .. mdp:: disre-tau - (0) \[ps\] + (0) [ps] time constant for distance restraints running average. A value of zero turns off time averaging. .. mdp:: nstdisreout - (100) \[steps\] + (100) [steps] period between steps when the running time-averaged and instantaneous distances of all atom pairs involved in restraints are written to the energy file (can make the energy file very @@ -2309,14 +2311,14 @@ NMR refinement .. mdp:: orire-fc - (0) \[kJ mol\] + (0) [kJ mol\ :sup:`-1`] force constant for orientation restraints, which is multiplied by a (possibly) different weight factor for each restraint, can be set to zero to obtain the orientations from a free simulation .. mdp:: orire-tau - (0) \[ps\] + (0) [ps] time constant for orientation restraints running average. A value of zero turns off time averaging. @@ -2330,7 +2332,7 @@ NMR refinement .. mdp:: nstorireout - (100) \[steps\] + (100) [steps] period between steps when the running time-averaged and instantaneous orientations for all restraints, and the molecular order tensor are written to the energy file (can make the energy @@ -2394,7 +2396,7 @@ Free energy calculations .. mdp:: fep-lambdas - \[array\] + [array] Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every :mdp:`nstdhdl` steps. Values must be between 0 and 1. Free energy differences @@ -2406,7 +2408,7 @@ Free energy calculations .. mdp:: coul-lambdas - \[array\] + [array] Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every :mdp:`nstdhdl` steps. Values must be between 0 and 1. Only the electrostatic @@ -2416,7 +2418,7 @@ Free energy calculations .. mdp:: vdw-lambdas - \[array\] + [array] Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every :mdp:`nstdhdl` steps. Values must be between 0 and 1. Only the van der Waals @@ -2425,7 +2427,7 @@ Free energy calculations .. mdp:: bonded-lambdas - \[array\] + [array] Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every :mdp:`nstdhdl` steps. Values must be between 0 and 1. Only the bonded interactions @@ -2433,7 +2435,7 @@ Free energy calculations .. mdp:: restraint-lambdas - \[array\] + [array] Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every :mdp:`nstdhdl` steps. Values must be between 0 and 1. Only the restraint @@ -2442,7 +2444,7 @@ Free energy calculations .. mdp:: mass-lambdas - \[array\] + [array] Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every :mdp:`nstdhdl` steps. Values must be between 0 and 1. Only the particle masses are @@ -2450,7 +2452,7 @@ Free energy calculations .. mdp:: temperature-lambdas - \[array\] + [array] Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every :mdp:`nstdhdl` steps. Values must be between 0 and 1. Only the temperatures @@ -2505,7 +2507,7 @@ Free energy calculations .. mdp:: sc-sigma - (0.3) \[nm\] + (0.3) [nm] the soft-core sigma for particles which have a C6 or C12 parameter equal to zero or a sigma smaller than :mdp:`sc-sigma` @@ -2878,12 +2880,12 @@ Expanded Ensemble calculations .. mdp:: sim-temp-low - (300) \[K\] + (300) [K] Low temperature for simulated tempering. .. mdp:: sim-temp-high - (300) \[K\] + (300) [K] High temperature for simulated tempering. .. mdp:: simulated-tempering-scaling @@ -2930,17 +2932,17 @@ Non-equilibrium MD .. mdp:: accelerate - (0) \[nm ps^-2\] + (0) [nm ps\ :sup:`-2`] acceleration for :mdp:`acc-grps`; x, y and z for each group (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has - constant acceleration of 0.1 nm ps-2 in X direction, second group + constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group the opposite). .. mdp:: freezegrps Groups that are to be frozen (*i.e.* their X, Y, and/or Z position will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim` - specifies for which dimension the freezing applies. To avoid + specifies for which dimension(s) the freezing applies. To avoid spurious contributions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time. Note that coordinates @@ -2956,7 +2958,7 @@ Non-equilibrium MD .. mdp:: cos-acceleration - (0) \[nm ps^-2\] + (0) [nm ps\ :sup:`-2`] the amplitude of the acceleration profile for calculating the viscosity. The acceleration is in the X-direction and the magnitude is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are @@ -2965,7 +2967,7 @@ Non-equilibrium MD .. mdp:: deform - (0 0 0 0 0 0) \[nm ps-1\] + (0 0 0 0 0 0) [nm ps\ :sup:`-1`] The velocities of deformation for the box elements: a(x) b(y) c(z) b(x) c(x) c(y). Each step the box elements for which :mdp:`deform` is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal @@ -2989,7 +2991,7 @@ Electric fields alternating and pulsed. The general expression for the field has the form of a gaussian laser pulse: - E(t) = E0 exp ( -(t-t0)^2/(2 sigma^2) ) cos(omega (t-t0)) + E(t) = E0 exp ( -(t-t0)\ :sup:`2`/(2 sigma\ :sup:`2`) ) cos(omega (t-t0)) For example, the four parameters for direction x are set in the three fields of :mdp:`electric-field-x` (and similar for y and z) @@ -3002,7 +3004,7 @@ Electric fields electric field is applied. More details in Carl Caleman and David van der Spoel: Picosecond - Melting of Ice by an Infrared Laser Pulse - A Simulation Study + Melting of Ice by an Infrared Laser Pulse - A Simulation Study. Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008) @@ -3066,27 +3068,27 @@ Mixed quantum/classical molecular dynamics .. mdp:: QMcharge - (0) \[integer\] + (0) [integer] 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. .. mdp:: QMmult - (1) \[integer\] + (1) [integer] The multiplicity of the :mdp:`QMMM-grps`. In case there are more than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer needs to be specified separately. .. mdp:: CASorbitals - (0) \[integer\] + (0) [integer] The number of orbitals to be included in the active space when doing a CASSCF computation. .. mdp:: CASelectrons - (0) \[integer\] + (0) [integer] The number of electrons to be included in the active space when doing a CASSCF computation. @@ -3164,7 +3166,7 @@ Electrophysiology" simulation setups. (See the `reference manual`_ for details). .. mdp:: coupl-steps - (\10) Average the number of ions per compartment over these many swap attempt steps. + (10) Average the number of ions per compartment over these many swap attempt steps. This can be used to prevent that ions near a compartment boundary (diffusing through a channel, e.g.) lead to unwanted back and forth swaps. @@ -3206,7 +3208,7 @@ Electrophysiology" simulation setups. (See the `reference manual`_ for details). .. mdp:: cyl0-r - (2.0) \[nm\] Radius of the split cylinder #0. + (2.0) [nm] Radius of the split cylinder #0. Two split cylinders (mimicking the channel pores) can optionally be defined relative to the center of the split group. With the help of these cylinders it can be counted which ions have passed which channel. The split cylinder @@ -3214,23 +3216,23 @@ Electrophysiology" simulation setups. (See the `reference manual`_ for details). .. mdp:: cyl0-up - (1.0) \[nm\] Upper extension of the split cylinder #0. + (1.0) [nm] Upper extension of the split cylinder #0. .. mdp:: cyl0-down - (1.0) \[nm\] Lower extension of the split cylinder #0. + (1.0) [nm] Lower extension of the split cylinder #0. .. mdp:: cyl1-r - (2.0) \[nm\] Radius of the split cylinder #1. + (2.0) [nm] Radius of the split cylinder #1. .. mdp:: cyl1-up - (1.0) \[nm\] Upper extension of the split cylinder #1. + (1.0) [nm] Upper extension of the split cylinder #1. .. mdp:: cyl1-down - (1.0) \[nm\] Lower extension of the split cylinder #1. + (1.0) [nm] Lower extension of the split cylinder #1. User defined thingies