.. mdp:: mts-level2-forces
- (longrange-nonbonded nonbonded pair dihedral)
- A list of force groups that will be evaluated only every
+ (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`` has to be entered here.
- The default value should work well for most standard atomistic simulations
- and in particular for replacing virtual site treatment for increasing
- the time step.
+ and/or LJ interactions, ``longrange-nonbonded`` can not be omitted here.
.. mdp:: mts-level2-factor
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.
+ 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
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
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
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
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
.. 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
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.
+ be in the slow level. This option requires :mdp-value:`awh-potential=umbrella`.
.. mdp:: awh1-dim1-coord-index
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)
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
with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
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.
+ 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>`.
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