.. 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)
.. 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` *
.. 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.
.. mdp:: nstcomm
- (100) \[steps\]
+ (100) [steps]
frequency for center of mass motion removal
.. mdp:: comm-grps
.. 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
.. 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.
.. 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
.. mdp:: rtpi
- (0.05) \[nm\]
+ (0.05) [nm]
the test particle insertion radius, see integrators
:mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
.. 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
.. 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
.. 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
.. mdp:: nstlist
- \(10) \[steps\]
+ (10) [steps]
.. mdp-value:: >0
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
.. 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
.. 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
: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.
: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.
.. 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
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
.. 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
.. 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.
.. 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
.. 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
.. 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
.. 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
.. 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
.. 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.
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
.. 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
.. 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`)
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|
.. 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`.
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.
.. mdp:: lincs-warnangle
- (30) \[deg\]
+ (30) [deg]
maximum angle that a bond can rotate before LINCS will complain
.. mdp:: morse
(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
.. 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
.. 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
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
.. 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
.. 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`.
.. 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`
.. 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
.. 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
.. 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
.. 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`
.. 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,
.. 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
.. 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
.. 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
.. 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
.. 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.
.. 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
.. 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
.. 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
.. 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
.. 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
.. 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
.. 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
.. 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
.. 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`
.. 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
.. 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
.. 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
.. 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
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)
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)
.. 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.
.. 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.
.. 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
.. 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
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff