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
.. 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
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
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