.. index:: fix restrain

fix restrain command
====================

Syntax
""""""

.. code-block:: LAMMPS

   fix ID group-ID restrain keyword args ...

* ID, group-ID are documented in :doc:`fix <fix>` command
* restrain = style name of this fix command
* one or more keyword/arg pairs may be appended
* keyword = *bond* or *lbound* or *angle* or *dihedral*

  .. parsed-literal::

       *bond* args = atom1 atom2 Kstart Kstop r0start (r0stop)
         atom1,atom2 = IDs of 2 atoms in bond
         Kstart,Kstop = restraint coefficients at start/end of run (energy units)
         r0start = equilibrium bond distance at start of run (distance units)
         r0stop = equilibrium bond distance at end of run (optional) (distance units). If not
           specified it is assumed to be equal to r0start
       *lbound* args = atom1 atom2 Kstart Kstop r0start (r0stop)
         atom1,atom2 = IDs of 2 atoms in bond
         Kstart,Kstop = restraint coefficients at start/end of run (energy units)
         r0start = equilibrium bond distance at start of run (distance units)
         r0stop = equilibrium bond distance at end of run (optional) (distance units). If not
           specified it is assumed to be equal to r0start
       *angle* args = atom1 atom2 atom3 Kstart Kstop theta0
         atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
         Kstart,Kstop = restraint coefficients at start/end of run (energy units)
         theta0 = equilibrium angle theta (degrees)
       *dihedral* args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
         atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
         Kstart,Kstop = restraint coefficients at start/end of run (energy units)
         phi0 = equilibrium dihedral angle phi (degrees)
         keyword/value = optional keyword value pairs. supported keyword/value pairs:
           *mult* n = dihedral multiplicity n (integer >= 0, default = 1)

Examples
""""""""

.. code-block:: LAMMPS

   fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
   fix holdem all restrain lbound 45 48 2000.0 2000.0 2.75
   fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
   fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
   fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0

Description
"""""""""""

Restrain the motion of the specified sets of atoms by making them part
of a bond or angle or dihedral interaction whose strength can vary
over time during a simulation.  This is functionally similar to
creating a bond or angle or dihedral for the same atoms in a data
file, as specified by the :doc:`read_data <read_data>` command, albeit
with a time-varying pre-factor coefficient, and except for exclusion
rules, as explained below.

For the purpose of force field parameter-fitting or mapping a molecular
potential energy surface, this fix reduces the hassle and risk
associated with modifying data files.  In other words, use this fix to
temporarily force a molecule to adopt a particular conformation.  To
create a permanent bond or angle or dihedral, you should modify the
data file.

.. note::

   Adding a bond/angle/dihedral with this command does not apply
   the exclusion rules and weighting factors specified by the
   :doc:`special_bonds <special_bonds>` command to atoms in the restraint
   that are now bonded (1-2,1-3,1-4 neighbors) as a result.  If they are
   close enough to interact in a :doc:`pair_style <pair_style>` sense
   (non-bonded interaction), then the bond/angle/dihedral restraint
   interaction will simply be superposed on top of that interaction.

The group-ID specified by this fix is ignored.

The second example above applies a restraint to hold the dihedral
angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
restraint coefficient.  The fourth example applies similar restraints
to multiple dihedral angles using a restraint coefficient that
increases from 0.0 to 2000.0 over the course of the run.

.. note::

   Adding a force to atoms implies a change in their potential
   energy as they move due to the applied force field.  For dynamics via
   the :doc:`run <run>` command, this energy can be added to the system's
   potential energy for thermodynamic output (see below).  For energy
   minimization via the :doc:`minimize <minimize>` command, this energy
   must be added to the system's potential energy to formulate a
   self-consistent minimization problem (see below).

In order for a restraint to be effective, the restraint force must
typically be significantly larger than the forces associated with
conventional force field terms.  If the restraint is applied during a
dynamics run (as opposed to during an energy minimization), a large
restraint coefficient can significantly reduce the stable timestep
size, especially if the atoms are initially far from the preferred
conformation.  You may need to experiment to determine what value of :math:`K`
works best for a given application.

For the case of finding a minimum energy structure for a single
molecule with particular restraints (e.g. for fitting force field
parameters or constructing a potential energy surface), commands such
as the following may be useful:

.. code-block:: LAMMPS

   # minimize molecule energy with restraints
   velocity all create 600.0 8675309 mom yes rot yes dist gaussian
   fix NVE all nve
   fix TFIX all langevin 600.0 0.0 100 24601
   fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2}
   fix_modify REST energy yes
   run 10000
   fix TFIX all langevin 0.0 0.0 100 24601
   fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${angle2}
   fix_modify REST energy yes
   run 10000
   # sanity check for convergence
   minimize 1e-6 1e-9 1000 100000
   # report unrestrained energies
   unfix REST
   run 0

----------

The *bond* keyword applies a bond restraint to the specified atoms
using the same functional form used by the :doc:`bond_style harmonic <bond_harmonic>` command.  The potential associated with
the restraint is

.. math::

   E = K (r - r_0)^2

with the following coefficients:

* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)

:math:`K` and :math:`r_0` are specified with the fix.  Note that the usual 1/2 factor
is included in :math:`K`.

----------

The *lbound* keyword applies a lower bound bond restraint to the specified atoms
using the same functional form used by the :doc:`bond_style harmonic <bond_harmonic>` command if the distance between
the atoms is smaller than the equilibrium bond distance and 0 otherwise. The potential associated with
the restraint is

.. math::

   E = K (r - r_0)^2 ,if\;r < r_0

.. math::

   E = 0 \qquad\quad\quad ,if\;r \ge r_0

with the following coefficients:

* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)

:math:`K` and :math:`r_0` are specified with the fix.  Note that the usual 1/2 factor
is included in :math:`K`.

----------

The *angle* keyword applies an angle restraint to the specified atoms
using the same functional form used by the :doc:`angle_style harmonic <angle_harmonic>` command.  The potential associated with
the restraint is

.. math::

   E = K (\theta - \theta_0)^2

with the following coefficients:

* :math:`K` (energy)
* :math:`\theta_0` (degrees)

:math:`K` and :math:`\theta_0` are specified with the fix.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence :math:`K` is effectively energy per
radian\^2.  Note that the usual 1/2 factor is included in :math:`K`.

----------

The *dihedral* keyword applies a dihedral restraint to the specified
atoms using a simplified form of the function used by the
:doc:`dihedral_style charmm <dihedral_charmm>` command.  The potential
associated with the restraint is

.. math::

   E = K [ 1 + \cos (n \phi - d) ]

with the following coefficients:

* :math:`K` (energy)
* :math:`n` (multiplicity, >= 0)
* :math:`d` (degrees) = :math:`\phi_0 + 180`

:math:`K` and :math:`\phi_0` are specified with the fix.  Note that the value of the
dihedral multiplicity :math:`n` is set by default to 1. You can use the
optional *mult* keyword to set it to a different positive integer.
Also note that the energy will be a minimum when the
current dihedral angle :math:`\phi` is equal to :math:`\phi_0`.

----------

Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

No information about this fix is written to :doc:`binary restart files
<restart>`.

The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy associated with this fix to the
global potential energy of the system as part of :doc:`thermodynamic
output <thermo_style>` The default setting for this fix is
:doc:`fix_modify energy no <fix_modify>`.

The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.

.. note::

   If you want the fictitious potential energy associated with the
   added forces to be included in the total potential energy of the
   system (the quantity being minimized), you MUST enable the
   :doc:`fix_modify <fix_modify>` *energy* option for this fix.

This fix computes a global scalar and a global vector of length 3,
which can be accessed by various :doc:`output commands <Howto_output>`.
The scalar is the total potential energy for *all* the restraints as
discussed above. The vector values are the sum of contributions to the
following individual categories:

* 1 = bond energy
* 2 = angle energy
* 3 = dihedral energy

The scalar and vector values calculated by this fix are "extensive".

No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

Restrictions
""""""""""""
 none

Related commands
""""""""""""""""

none


Default
"""""""

none
