See the "run control" section for a working example of the
syntax to use when making .mdp entries, with and without detailed
documentation for values those entries might take. Everything can
- be cross-referenced, see the examples there. TODO Make more
- cross-references.
+ be cross-referenced, see the examples there.
+
+.. todo:: Make more cross-references.
Molecular dynamics parameters (.mdp options)
============================================
of motion. For constant NVE simulations started from
corresponding points in the same trajectory, the trajectories
are analytically, but not binary, identical to the
- :mdp-value:`integrator=md` leap-frog integrator. The the kinetic
+ :mdp-value:`integrator=md` leap-frog integrator. The kinetic
energy, which is determined from the whole step velocities and
is therefore slightly too high. The advantage of this integrator
is more accurate, reversible Nose-Hoover and Parrinello-Rahman
significant part of the simulation time. The temperature for one
or more groups of atoms (:mdp:`tc-grps`) is set with
:mdp:`ref-t`, the inverse friction constant for each group is
- set with :mdp:`tau-t`. The parameter :mdp:`tcoupl` is
- ignored. The random generator is initialized with
+ set with :mdp:`tau-t`. The parameters :mdp:`tcoupl` and :mdp:`nsttcouple`
+ are ignored. The random generator is initialized with
:mdp:`ld-seed`. When used as a thermostat, an appropriate value
for :mdp:`tau-t` is 2 ps, since this results in a friction that
is lower than the internal friction of water, while it is high
same simulation. This option is generally useful to set only
when coping with a crashed simulation where files were lost.
+.. mdp:: mts
+
+ .. mdp-value:: no
+
+ Evaluate all forces at every integration step.
+
+ .. mdp-value:: yes
+
+ Use a multiple timing-stepping integrator to evaluate some forces, as specified
+ by :mdp:`mts-level2-forces` every :mdp:`mts-level2-factor` integration
+ steps. All other forces are evaluated at every step. MTS is currently
+ only supported with :mdp-value:`integrator=md`.
+
+.. mdp:: mts-levels
+
+ (2)
+ The number of levels for the multiple time-stepping scheme.
+ Currently only 2 is supported.
+
+.. mdp:: mts-level2-forces
+
+ (longrange-nonbonded)
+ A list of one or more force groups that will be evaluated only every
+ :mdp:`mts-level2-factor` steps. Supported entries are:
+ ``longrange-nonbonded``, ``nonbonded``, ``pair``, ``dihedral``, ``angle``,
+ ``pull`` and ``awh``. With ``pair`` the listed pair forces (such as 1-4)
+ are selected. With ``dihedral`` all dihedrals are selected, including cmap.
+ All other forces, including all restraints, are evaluated and
+ integrated every step. When PME or Ewald is used for electrostatics
+ and/or LJ interactions, ``longrange-nonbonded`` can not be omitted here.
+
+.. mdp:: mts-level2-factor
+
+ (2) [steps]
+ Interval for computing the forces in level 2 of the multiple time-stepping
+ scheme
+
.. mdp:: comm-mode
.. mdp-value:: Linear
(0) [steps]
number of steps that elapse between writing coordinates to the output
trajectory file (:ref:`trr`), the last coordinates are always written
+ unless 0, which means coordinates are not written into the trajectory
+ file.
.. mdp:: nstvout
(0) [steps]
number of steps that elapse between writing velocities to the output
trajectory file (:ref:`trr`), the last velocities are always written
+ unless 0, which means velocities are not written into the trajectory
+ file.
.. mdp:: nstfout
(0) [steps]
number of steps that elapse between writing forces to the output
- trajectory file (:ref:`trr`), the last forces are always written.
+ trajectory file (:ref:`trr`), the last forces are always written,
+ unless 0, which means forces are not written into the trajectory
+ file.
.. mdp:: nstlog
(1000) [steps]
number of steps that elapse between writing energies to the log
- file, the last energies are always written
+ file, the last energies are always written.
.. mdp:: nstcalcenergy
(0) [steps]
number of steps that elapse between writing position coordinates
- using lossy compression (:ref:`xtc` file)
+ using lossy compression (:ref:`xtc` file), 0 for not writing
+ compressed coordinates output.
.. mdp:: compressed-x-precision
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. With energy minimization this parameter
+ is not used as the pair list is updated when at least one atom
+ has moved by more than half the pair list buffer size.
.. 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
Unused.
-.. mdp:: ns-type
-
- .. mdp-value:: grid
-
- Make a grid in the box and only check atoms in neighboring grid
- cells when constructing a new neighbor list every
- :mdp:`nstlist` steps. In large systems grid search is much
- faster than simple search.
-
- .. mdp-value:: simple
-
- Check every atom in the box when constructing a new neighbor
- list every :mdp:`nstlist` steps (only with :mdp-value:`cutoff-scheme=group`
- cut-off scheme).
-
.. mdp:: pbc
.. mdp-value:: xyz
(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:: rlist
(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:`rlist` is ignored.
+ Cut-off distance for the short-range neighbor list. With dynamics,
+ this is by default set by the :mdp:`verlet-buffer-tolerance` option
+ and the value of :mdp:`rlist` is ignored. Without dynamics, this
+ is by default set to the maximum cut-off plus 5% buffer, except
+ for test particle insertion, where the buffer is managed exactly
+ and automatically. For NVE simulations, where the automated
+ setting is not possible, the advised procedure is to run :ref:`gmx grompp`
+ with an NVT setup with the expected temperature and copy the resulting
+ value of :mdp:`rlist` to the NVE setup.
Electrostatics
:mdp:`epsilon-rf`. The dielectric constant can be set to
infinity by setting :mdp:`epsilon-rf` =0.
- .. mdp-value:: Generalized-Reaction-Field
-
- Generalized reaction field with Coulomb cut-off
- :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rcoulomb`. The
- dielectric constant beyond the cut-off is
- :mdp:`epsilon-rf`. The ionic strength is computed from the
- number of charged (*i.e.* with non zero charge) charge
- groups. The temperature for the GRF potential is set with
- :mdp:`ref-t`.
-
- .. 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:: coulomb-modifier
- .. mdp-value:: Potential-shift-Verlet
-
- Selects Potential-shift with the Verlet cutoff-scheme, as it is
- (nearly) free; selects None with the group cutoff-scheme.
-
.. mdp-value:: Potential-shift
Shift the Coulomb potential by a constant such that it is zero
.. mdp-value:: None
- 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 pair list.
+ Use an unmodified Coulomb potential. This can be useful
+ when comparing energies with those computed with other software.
.. mdp:: rcoulomb-switch
: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
.. mdp:: vdw-modifier
- .. mdp-value:: Potential-shift-Verlet
-
- Selects Potential-shift with the Verlet cutoff-scheme, as it is
- (nearly) free; selects None with the group cutoff-scheme.
-
.. mdp-value:: Potential-shift
Shift the Van der Waals potential by a constant such that it is
.. mdp-value:: None
- 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 pair list.
+ Use an unmodified Van der Waals potential. This can be useful
+ when comparing energies with those computed with other software.
.. mdp-value:: Force-switch
(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
+ can give pairs of energy groups for which separate user tables
should be used. The two energy groups will be appended to the table
file name, in order of their definition in :mdp:`energygrps`,
- seperated by underscores. For example, if ``energygrps = Na Cl
+ separated by underscores. For example, if ``energygrps = Na Cl
Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
normal ``table.xvg`` which will be used for all other energy group
.. mdp-value:: 3dc
The reciprocal sum is still performed in 3D, but a force and
- potential correction applied in the `z` dimension to produce a
+ potential correction applied in the ``z`` dimension to produce a
pseudo-2D summation. If your system has a slab geometry in the
- `x-y` plane you can try to increase the `z`-dimension of the box
+ ``x-y`` plane you can try to increase the ``z``-dimension of the box
(a box height of 3 times the slab height is usually ok) and use
this option.
(-1)
The frequency for coupling the temperature. The default value of -1
- sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
- :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
+ sets :mdp:`nsttcouple` equal to 10, or fewer steps if required
+ for accurate integration. Note that the default value is not 1
+ because additional computation and communication is required for
+ obtaining the kinetic energy. For velocity
Verlet integrators :mdp:`nsttcouple` is set to 1.
.. mdp:: nh-chain-length
integrators, the leap-frog :mdp-value:`integrator=md` integrator
only supports 1. Data for the NH chain variables is not printed
to the :ref:`edr` file by default, but can be turned on with the
- :mdp:`print-nose-hoover-chains` option.
+ :mdp:`print-nose-hoover-chain-variables` option.
.. mdp:: print-nose-hoover-chain-variables
ensemble, but it is the most efficient way to scale a box at the
beginning of a run.
+ .. mdp-value:: C-rescale
+
+ Exponential relaxation pressure coupling with time constant
+ :mdp:`tau-p`, including a stochastic term to enforce correct
+ volume fluctuations. The box is scaled every :mdp:`nstpcouple`
+ steps. It can be used for both equilibration and production.
+
.. mdp-value:: Parrinello-Rahman
Extended-ensemble pressure coupling where the box vectors are
.. mdp-value:: surface-tension
Surface tension coupling for surfaces parallel to the
- xy-plane. Uses normal pressure coupling for the `z`-direction,
- while the surface tension is coupled to the `x/y` dimensions of
+ xy-plane. Uses normal pressure coupling for the ``z``-direction,
+ while the surface tension is coupled to the ``x/y`` dimensions of
the box. The first :mdp:`ref-p` value is the reference surface
tension times the number of surfaces ``bar nm``, the second
- value is the reference `z`-pressure ``bar``. The two
+ value is the reference ``z``-pressure ``bar``. The two
:mdp:`compressibility` values are the compressibility in the
- `x/y` and `z` direction respectively. The value for the
- `z`-compressibility should be reasonably accurate since it
+ ``x/y`` and ``z`` direction respectively. The value for the
+ ``z``-compressibility should be reasonably accurate since it
influences the convergence of the surface-tension, it can also
be set to zero to have a box with constant height.
(-1)
The frequency for coupling the pressure. The default value of -1
- sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
- :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
+ sets :mdp:`nstpcouple` equal to 10, or fewer steps if required
+ for accurate integration. Note that the default value is not 1
+ because additional computation and communication is required for
+ obtaining the virial. For velocity
Verlet integrators :mdp:`nstpcouple` is set to 1.
.. mdp:: tau-p
The reference coordinates for position restraints are not
modified. Note that with this option the virial and pressure
- will depend on the absolute positions of the reference
- coordinates.
+ might be ill defined, see :ref:`here <reference-manual-position-restraints>`
+ for more details.
.. mdp-value:: all
one COM is used, even when there are multiple molecules with
position restraints. For calculating the COM of the reference
coordinates in the starting configuration, periodic boundary
- conditions are not taken into account.
+ conditions are not taken into account. Note that with this option
+ the virial and pressure might be ill defined, see
+ :ref:`here <reference-manual-position-restraints>` for more details.
Simulated annealing
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
COM pulling
^^^^^^^^^^^
+Sets whether pulling on collective variables is active.
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
Center of mass pulling using a constraint between the reference
group and one or more groups. The setup is identical to the
option umbrella, except for the fact that a rigid constraint is
- applied instead of a harmonic potential.
+ applied instead of a harmonic potential. Note that this type is
+ not supported in combination with multiple time stepping.
.. mdp-value:: constant-force
.. mdp-value:: direction-periodic
- 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
+ As :mdp-value:`pull-coord1-geometry=direction`, but does not apply
+ periodic box vector corrections to keep the distance within half
+ the box length. This is (only) useful for pushing groups apart
+ by more than half the box length by continuously changing the reference
+ location using a pull rate. 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.
+ the pull force is not added to the virial.
.. mdp-value:: direction-relative
then defined as the angle between two planes: the plane spanned by the
the two first vectors and the plane spanned the two last vectors.
+ .. mdp-value:: transformation
+
+ Transforms other pull coordinates using a mathematical expression defined by :mdp:`pull-coord1-expression`.
+ Pull coordinates of lower indices can be used as variables to this pull coordinate.
+ Thus, pull transformation coordinates should have a higher pull coordinate index
+ than all pull coordinates they transform.
+
+.. mdp:: pull-coord1-expression
+
+ Mathematical expression to transform pull coordinates of lower indices to a new one.
+ The pull coordinates are referred to as variables in the equation so that
+ pull-coord1's value becomes 'x1', pull-coord2 value becomes 'x2' etc.
+ The mathematical expression are evaluated using muParser.
+ Only relevant if :mdp:`pull-coord1-geometry` is set to :mdp-value:`transformation`.
+
+.. mdp:: pull-coord1-dx
+
+ (1e-9)
+ Size of finite difference to use in numerical derivation of the pull coordinate
+ with respect to other pull coordinates.
+ The current implementation uses a simple first order finite difference method to perform derivation so that
+ f'(x) = (f(x+dx)-f(x))/dx
+ Only relevant if :mdp:`pull-coord1-geometry` is set to :mdp-value:`transformation`.
.. mdp:: pull-coord1-groups
multidimensional and is defined by mapping each dimension to a pull coordinate index.
This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
:mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
- indices.
+ indices. Pull geometry 'direction-periodic' is not supported by AWH.
.. mdp:: awh-potential
The applied biasing potential is the convolution of the bias function and a
set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
in a smooth potential function and force. The resolution of the potential is set
- by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
+ by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`. This option is not
+ compatible with using the free energy lambda state as an AWH reaction coordinate.
.. mdp-value:: umbrella
using Monte-Carlo sampling. The force constant is set with
:mdp:`awh1-dim1-force-constant`. The umbrella location
is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
- There are no advantages to using an umbrella.
- This option is mainly for comparison and testing purposes.
+ This is option is required when using the free energy lambda state as an AWH reaction coordinate.
+ Apart from that, this option is mainly for comparison
+ and testing purposes as there are no advantages to using an umbrella.
.. mdp:: awh-share-multisim
The file name can be changed with the ``-awh`` option.
The first :mdp:`awh1-ndim` columns of
each input file should contain the coordinate values, such that each row defines a point in
- coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
+ coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value (in kT) for each point.
The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
be in the same column as written by :ref:`gmx awh`.
.. mdp-value:: positive
- Share the bias and PMF estimates within and/or between simulations.
- Within a simulation, the bias will be shared between biases that have the
- same :mdp:`awh1-share-group` index (note that the current code does not support this).
- With :mdp-value:`awh-share-multisim=yes` and
- :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
+ Share the bias and PMF estimates between simulations. This currently
+ only works between biases with the same index. Note that currently
+ sharing within a single simulation is not supported.
+ The bias will be shared across simulations that specify the same
+ value for :mdp:`awh1-share-group`. To enable this, use
+ :mdp-value:`awh-share-multisim=yes` and the :ref:`gmx mdrun` option
+ ``-multidir``.
Sharing may increase convergence initially, although the starting configurations
can be critical, especially when sharing between many biases.
- Currently, positive group values should start at 1 and increase
- by 1 for each subsequent bias that is shared.
.. mdp:: awh1-ndim
.. mdp-value:: pull
- The module providing the reaction coordinate for this dimension.
- Currently AWH can only act on pull coordinates.
+ The pull module is providing the reaction coordinate for this dimension.
+ With multiple time-stepping, AWH and pull should be in the same MTS level.
+
+ .. mdp-value:: fep-lambda
+
+ The free energy lambda state is the reaction coordinate for this dimension.
+ The lambda states to use are specified by :mdp:`fep-lambdas`, :mdp:`vdw-lambdas`,
+ :mdp:`coul-lambdas` etc. This is not compatible with delta-lambda. It also requires
+ calc-lambda-neighbors to be -1. With multiple time-stepping, AWH should
+ be in the slow level. This option requires :mdp-value:`awh-potential=umbrella`.
.. mdp:: awh1-dim1-coord-index
(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`
+ For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
is allowed. The interval will then wrap around from +period/2 to -period/2.
+ For the direction geometry, the dimension is made periodic when
+ the direction is along a box vector and covers more than 95%
+ of the box length. Note that one should not apply pressure coupling
+ along a periodic dimension.
.. mdp:: awh1-dim1-end
(0.0) [nm] or [rad]
End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
-.. mdp:: awh1-dim1-period
-
- (0.0) [nm] or [rad]
- The period of this reaction coordinate, use 0 when the coordinate is not periodic.
-
.. mdp:: awh1-dim1-diffusion
- (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps]
+ (10\ :sup:`-5`) [nm\ :sup:`2`/ps], [rad\ :sup:`2`/ps] or [ps\ :sup:`-1`]
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,
(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`
+ (possibly) different factor for each restraint given in the ``fac``
column of the interaction in the topology file.
.. mdp:: disre-tau
written out. For normal BAR such as with :ref:`gmx bar`, a value of
1 is sufficient, while for MBAR -1 should be used.
+.. mdp:: sc-function
+
+ (beutler)
+
+ .. mdp-value:: beutler
+
+ Beutler *et al.* soft-core function
+
+ .. mdp-value:: gapsys
+
+ Gapsys *et al.* soft-core function
+
.. mdp:: sc-alpha
(0)
- the soft-core alpha parameter, a value of 0 results in linear
- interpolation of the LJ and Coulomb interactions
+ for `sc-function=beutler` the soft-core alpha parameter,
+ a value of 0 results in linear interpolation of the
+ LJ and Coulomb interactions.
+ Used only with `sc-function=beutler`
.. mdp:: sc-r-power
(6)
- the power of the radial term in the soft-core equation. Possible
- values are 6 and 48. 6 is more standard, and is the default. When
- 48 is used, then sc-alpha should generally be much lower (between
- 0.001 and 0.003).
+ power 6 for the radial term in the soft-core equation.
+ Used only with `sc-function=beutler`
.. mdp:: sc-coul
states are used, not with :mdp:`couple-lambda0` /
:mdp:`couple-lambda1`, and you can still turn off soft-core
interactions by setting :mdp:`sc-alpha` to 0.
+ Used only with `sc-function=beutler`
.. mdp:: sc-power
(0)
the power for lambda in the soft-core function, only the values 1
- and 2 are supported
+ and 2 are supported. Used only with `sc-function=beutler`
.. mdp:: sc-sigma
(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`
+ for `sc-function=beutler` the soft-core sigma for particles
+ which have a C6 or C12 parameter equal to zero or a sigma smaller
+ than :mdp:`sc-sigma`.
+ Used only with `sc-function=beutler`
+
+.. mdp:: sc-gapsys-scale-linpoint-lj
+
+ (0.85)
+ for `sc-function=gapsys` it is the unitless alphaLJ parameter.
+ It controls the softness of the van der Waals interactions
+ by scaling the point for linearizing the vdw force.
+ Setting it to 0 will result in the standard hard-core
+ van der Waals interactions.
+ Used only with `sc-function=gapsys`
+
+.. mdp:: sc-gapsys-scale-linpoint-q
+
+ (0.3) [nm/e^2]
+ For `sc-function=gapsys` the alphaQ parameter
+ with the unit of [nm/e^2] and default value of 0.3. It controls
+ the softness of the Coulombic interactions. Setting it to 0 will
+ result in the standard hard-core Coulombic interactions.
+ Used only with `sc-function=gapsys`
+
+.. mdp:: sc-gapsys-sigma-lj
+
+ (0.3) [nm]
+ for `sc-function=gapsys` the soft-core sigma for particles
+ which have a C6 or C12 parameter equal to zero.
+ Used only with `sc-function=gapsys`
.. mdp:: couple-moltype
groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
in groups Protein and Sol will experience constant acceleration as
- specified in the :mdp:`accelerate` line
+ specified in the :mdp:`accelerate` line. Note that the kinetic energy
+ of the center of mass of accelarated groups contributes to the kinetic
+ energy and temperature of the system. If this is not desired, make
+ each accelerate group also a separate temperature coupling group.
.. mdp:: accelerate
.. mdp:: freezedim
dimensions for which groups in :mdp:`freezegrps` should be frozen,
- specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
- N N N N`` means that particles in the first group can move only in
+ specify ``Y`` or ``N`` for X, Y and Z and for each group (*e.g.*
+ ``Y Y N N N N`` means that particles in the first group can move only in
Z direction. The particles in the second group can move in any
direction).
Electric fields
^^^^^^^^^^^^^^^
-.. mdp:: electric-field-x ; electric-field-y ; electric-field-z
+.. mdp:: electric-field-x
+.. mdp:: electric-field-y
+.. mdp:: electric-field-z
Here you can specify an electric field that optionally can be
alternating and pulsed. The general expression for the field
has the form of a gaussian laser pulse:
- E(t) = E0 exp ( -(t-t0)\ :sup:`2`/(2 sigma\ :sup:`2`) ) cos(omega (t-t0))
+ .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
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)
- like
+ fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
+ and ``electric-field-z``) like
- electric-field-x = E0 omega t0 sigma
+ ``electric-field-x = E0 omega t0 sigma``
- In the special case that sigma = 0, the exponential term is omitted
- and only the cosine term is used. If also omega = 0 a static
- electric field is applied.
+ with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
- More details in Carl Caleman and David van der Spoel: Picosecond
- Melting of Ice by an Infrared Laser Pulse - A Simulation Study.
- Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008)
+ In the special case that ``sigma = 0``, the exponential term is omitted
+ and only the cosine term is used. In this case, ``t0`` must be set to 0.
+ If also ``omega = 0`` a static electric field is applied.
+ Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
Mixed quantum/classical molecular dynamics
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-.. MDP:: QMMM
-
- .. mdp-value:: no
-
- No QM/MM.
-
- .. mdp-value:: yes
-
- Do a QM/MM simulation. Several groups can be described at
- different QM levels separately. These are specified in the
- :mdp:`QMMM-grps` field separated by spaces. The level of *ab
- initio* theory at which the groups are described is specified by
- :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
- groups at different levels of theory is only possible with the
- ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
-
.. mdp:: QMMM-grps
- groups to be descibed at the QM level (works also in case of MiMiC QM/MM)
-
-.. mdp:: QMMMscheme
-
- .. mdp-value:: normal
-
- normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
- modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
- *ab initio* theory. The rest of the system is described at the
- MM level. The QM and MM subsystems interact as follows: MM point
- charges are included in the QM one-electron hamiltonian and all
- Lennard-Jones interactions are described at the MM level.
-
- .. mdp-value:: ONIOM
-
- The interaction between the subsystem is described using the
- ONIOM method by Morokuma and co-workers. There can be more than
- one :mdp:`QMMM-grps` each modeled at a different level of QM
- theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
-
-.. mdp:: QMmethod
-
- (RHF)
- Method used to compute the energy and gradients on the QM
- atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
- CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
- included in the active space is specified by :mdp:`CASelectrons`
- and :mdp:`CASorbitals`.
-
-.. mdp:: QMbasis
-
- (STO-3G)
- Basis set used to expand the electronic wavefuntion. Only Gaussian
- basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
- 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
+ groups to be descibed at the QM level for MiMiC QM/MM
-.. mdp:: QMcharge
-
- (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]
- 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]
- The number of orbitals to be included in the active space when
- doing a CASSCF computation.
-
-.. mdp:: CASelectrons
-
- (0) [integer]
- The number of electrons to be included in the active space when
- doing a CASSCF computation.
-
-.. MDP:: SH
+.. MDP:: QMMM
.. mdp-value:: no
- No surface hopping. The system is always in the electronic
- ground-state.
-
- .. mdp-value:: yes
-
- Do a QM/MM MD simulation on the excited state-potential energy
- surface and enforce a *diabatic* hop to the ground-state when
- the system hits the conical intersection hyperline in the course
- the simulation. This option only works in combination with the
- CASSCF method.
-
+ QM/MM is no longer supported via these .mdp options. For MiMic, use no here.
Computational Electrophysiology
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
(1.0) [nm] Lower extension of the split cylinder #1.
+Density-guided simulations
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+These options enable and control the calculation and application of additional
+forces that are derived from three-dimensional densities, e.g., from cryo
+electron-microscopy experiments. (See the `reference manual`_ for details)
+
+.. mdp:: density-guided-simulation-active
+
+ (no) Activate density-guided simulations.
+
+.. mdp:: density-guided-simulation-group
+
+ (protein) The atoms that are subject to the forces from the density-guided
+ simulation and contribute to the simulated density.
+
+.. mdp:: density-guided-simulation-similarity-measure
+
+ (inner-product) Similarity measure between the density that is calculated
+ from the atom positions and the reference density.
+
+ .. mdp-value:: inner-product
+
+ Takes the sum of the product of reference density and simulated density
+ voxel values.
+
+ .. mdp-value:: relative-entropy
+
+ Uses the negative relative entropy (or Kullback-Leibler divergence)
+ between reference density and simulated density as similarity measure.
+ Negative density values are ignored.
+
+ .. mdp-value:: cross-correlation
+
+ Uses the Pearson correlation coefficient between reference density and
+ simulated density as similarity measure.
+
+.. mdp:: density-guided-simulation-atom-spreading-weight
+
+ (unity) Determines the multiplication factor for the Gaussian kernel when
+ spreading atoms on the grid.
+
+ .. mdp-value:: unity
+
+ Every atom in the density fitting group is assigned the same unit factor.
+
+ .. mdp-value:: mass
+
+ Atoms contribute to the simulated density proportional to their mass.
+
+ .. mdp-value:: charge
+
+ Atoms contribute to the simulated density proportional to their charge.
+
+.. mdp:: density-guided-simulation-force-constant
+
+ (1e+09) [kJ mol\ :sup:`-1`] The scaling factor for density-guided simulation
+ forces. May also be negative.
+
+.. mdp:: density-guided-simulation-gaussian-transform-spreading-width
+
+ (0.2) [nm] The Gaussian RMS width for the spread kernel for the simulated
+ density.
+
+.. mdp:: density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width
+
+ (4) The range after which the gaussian is cut off in multiples of the Gaussian
+ RMS width described above.
+
+.. mdp:: density-guided-simulation-reference-density-filename
+
+ (reference.mrc) Reference density file name using an absolute path or a path
+ relative to the to the folder from which :ref:`gmx mdrun` is called.
+
+.. mdp:: density-guided-simulation-nst
+
+ (1) Interval in steps at which the density fitting forces are evaluated
+ and applied. The forces are scaled by this number when applied (See the
+ `reference manual`_ for details).
+
+.. mdp:: density-guided-simulation-normalize-densities
+
+ (true) Normalize the sum of density voxel values to one for the reference
+ density as well as the simulated density.
+
+.. mdp:: density-guided-simulation-adaptive-force-scaling
+
+ (false) Adapt the force constant to ensure a steady increase in similarity
+ between simulated and reference density.
+
+ .. mdp-value: false
+
+ Do not use adaptive force scaling.
+
+ .. mdp-value:: true
+
+ Use adaptive force scaling.
+
+.. mdp:: density-guided-simulation-adaptive-force-scaling-time-constant
+
+ (4) [ps] Couple force constant to increase in similarity with reference density
+ with this time constant. Larger times result in looser coupling.
+
+.. mdp:: density-guided-simulation-shift-vector
+
+ (0,0,0) [nm] Add this vector to all atoms in the
+ density-guided-simulation-group before calculating forces and energies for
+ density-guided-simulations. Affects only the density-guided-simulation forces
+ and energies. Corresponds to a shift of the input density in the opposite
+ direction by (-1) * density-guided-simulation-shift-vector.
+
+.. mdp:: density-guided-simulation-transformation-matrix
+
+ (1,0,0,0,1,0,0,0,1) Multiply all atoms with this matrix in the
+ density-guided-simulation-group before calculating forces and energies for
+ density-guided-simulations. Affects only the density-guided-simulation forces
+ and energies. Corresponds to a transformation of the input density by the
+ inverse of this matrix. The matrix is given in row-major order.
+ This option allows, e.g., rotation of the density-guided atom group around the
+ z-axis by :math:`\theta` degress by using following input:
+ :math:`(\cos \theta , -\sin \theta , 0 , \sin \theta , \cos \theta , 0 , 0 , 0 , 1)` .
+
+QM/MM simulations with CP2K Interface
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+These options enable and control the calculation and application of additional
+QM/MM forces that are computed by the CP2K package if it is linked into |Gromacs|.
+For further details about QM/MM interface implementation follow :ref:`qmmm`.
+
+.. mdp:: qmmm-cp2k-active
+
+ (false) Activate QM/MM simulations. Requires CP2K to be linked with |Gromacs|
+
+.. mdp:: qmmm-cp2k-qmgroup
+
+ (System) Index group with atoms that are treated with QM.
+
+.. mdp:: qmmm-cp2k-qmmethod
+
+ (PBE) Method used to describe the QM part of the system.
+
+ .. mdp-value:: PBE
+
+ DFT using PBE functional and DZVP-MOLOPT basis set.
+
+ .. mdp-value:: BLYP
+
+ DFT using BLYP functional and DZVP-MOLOPT basis set.
+
+ .. mdp-value:: INPUT
+
+ Provide an external input file for CP2K when running :ref:`gmx grompp` with the ``-qmi`` command-line option.
+ External input files are subject to the limitations that are described in :ref:`qmmm`.
+
+.. mdp:: qmmm-cp2k-qmcharge
+
+ (0) Total charge of the QM part.
+
+.. mdp:: qmmm-cp2k-qmmultiplicity
+
+ (1) Multiplicity or spin-state of QM part. Default value 1 means singlet state.
+
+.. mdp:: qmmm-cp2k-qmfilenames
+
+ () Names of the CP2K files that will be generated during the simulation.
+ When using the default, empty, value the name of the simulation input file will be used
+ with an additional ``_cp2k`` suffix.
User defined thingies
^^^^^^^^^^^^^^^^^^^^^
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff