forked from lijiext/lammps
210 lines
7.1 KiB
Plaintext
210 lines
7.1 KiB
Plaintext
.. index:: fix restrain
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fix restrain command
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====================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID restrain keyword args ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* restrain = style name of this fix command
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* one or more keyword/arg pairs may be appended
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* keyword = *bond* or *angle* or *dihedral*
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.. parsed-literal::
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*bond* args = atom1 atom2 Kstart Kstop r0
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atom1,atom2 = IDs of 2 atoms in bond
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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r0 = equilibrium bond distance (distance units)
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*angle* args = atom1 atom2 atom3 Kstart Kstop theta0
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atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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theta0 = equilibrium angle theta (degrees)
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*dihedral* args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
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atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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phi0 = equilibrium dihedral angle phi (degrees)
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Examples
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""""""""
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.. parsed-literal::
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fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
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fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
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fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
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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
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Description
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"""""""""""
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Restrain the motion of the specified sets of atoms by making them part
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of a bond or angle or dihedral interaction whose strength can vary
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over time during a simulation. This is functionally equivalent to
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creating a bond or angle or dihedral for the same atoms in a data
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file, as specified by the :doc:`read_data <read_data>` command, albeit
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with a time-varying pre-factor coefficient. For the purpose of
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forcefield parameter-fitting or mapping a molecular potential energy
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surface, this fix reduces the hassle and risk associated with
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modifying data files. In other words, use this fix to temporarily
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force a molecule to adopt a particular conformation. To create a
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permanent bond or angle or dihedral, you should modify the data file.
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The group-ID specified by this fix is ignored.
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The second example above applies a restraint to hold the dihedral
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angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
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restraint coefficient. The fourth example applies similar restraints
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to multiple dihedral angles using a restraint coefficient that
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increases from 0.0 to 2000.0 over the course of the run.
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.. note::
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Adding a force to atoms implies a change in their potential
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energy as they move due to the applied force field. For dynamics via
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the :doc:`run <run>` command, this energy can be added to the system's
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potential energy for thermodynamic output (see below). For energy
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minimization via the :doc:`minimize <minimize>` command, this energy
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must be added to the system's potential energy to formulate a
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self-consistent minimization problem (see below).
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In order for a restraint to be effective, the restraint force must
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typically be significantly larger than the forces associated with
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conventional forcefield terms. If the restraint is applied during a
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dynamics run (as opposed to during an energy minimization), a large
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restraint coefficient can significantly reduce the stable timestep
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size, especially if the atoms are initially far from the preferred
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conformation. You may need to experiment to determine what value of K
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works best for a given application.
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For the case of finding a minimum energy structure for a single
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molecule with particular restratins (e.g. for fitting forcefield
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parameters or constructing a potential energy surface), commands such
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as the following may be useful:
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.. parsed-literal::
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# minimize molecule energy with restraints
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velocity all create 600.0 8675309 mom yes rot yes dist gaussian
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fix NVE all nve
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fix TFIX all langevin 600.0 0.0 100 24601
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fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2}
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fix_modify REST energy yes
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run 10000
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fix TFIX all langevin 0.0 0.0 100 24601
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fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${angle2}
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fix_modify REST energy yes
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run 10000
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# sanity check for convergence
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minimize 1e-6 1e-9 1000 100000
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# report unrestrained energies
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unfix REST
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run 0
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----------
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The *bond* keyword applies a bond restraint to the specified atoms
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using the same functional form used by the :doc:`bond_style harmonic <bond_harmonic>` command. The potential associated with
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the restraint is
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.. image:: Eqs/bond_harmonic.jpg
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:align: center
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with the following coefficients:
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* K (energy/distance^2)
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* r0 (distance)
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K and r0 are specified with the fix. Note that the usual 1/2 factor
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is included in K.
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----------
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The *angle* keyword applies an angle restraint to the specified atoms
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using the same functional form used by the :doc:`angle_style harmonic <angle_harmonic>` command. The potential associated with
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the restraint is
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.. image:: Eqs/angle_harmonic.jpg
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:align: center
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with the following coefficients:
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* K (energy/radian^2)
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* theta0 (degrees)
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K and theta0 are specified with the fix. Note that the usual 1/2
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factor is included in K.
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----------
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The *dihedral* keyword applies a dihedral restraint to the specified
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atoms using a simplified form of the function used by the
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:doc:`dihedral_style charmm <dihedral_charmm>` command. The potential
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associated with the restraint is
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.. image:: Eqs/dihedral_charmm.jpg
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:align: center
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with the following coefficients:
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* K (energy)
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* n = 1
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* d (degrees) = phi0 + 180
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K and phi0 are specified with the fix. Note that the value of n is
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hard-wired to 1. Also note that the energy will be a minimum when the
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current dihedral angle phi is equal to phi0.
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`.
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The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
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fix to add the potential energy associated with this fix to the
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system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
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.. note::
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If you want the fictitious potential energy associated with the
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added forces to be included in the total potential energy of the
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system (the quantity being minimized), you MUST enable the
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:doc:`fix_modify <fix_modify>` *energy* option for this fix.
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This fix computes a global scalar, which can be accessed by various
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:ref:`output commands <howto_15>`. The scalar is the
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potential energy for all the restraints as discussed above. The scalar
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value calculated by this fix is "extensive".
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command.
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Restrictions
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""""""""""""
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none
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**Related commands:** none
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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