100 lines
3.3 KiB
ReStructuredText
100 lines
3.3 KiB
ReStructuredText
.. index:: fix spring/rg
|
|
|
|
fix spring/rg command
|
|
=====================
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
fix ID group-ID spring/rg K RG0
|
|
|
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
|
* spring/rg = style name of this fix command
|
|
* K = harmonic force constant (force/distance units)
|
|
* RG0 = target radius of gyration to constrain to (distance units)
|
|
|
|
.. parsed-literal::
|
|
|
|
if RG0 = NULL, use the current RG as the target value
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
.. code-block:: LAMMPS
|
|
|
|
fix 1 protein spring/rg 5.0 10.0
|
|
fix 2 micelle spring/rg 5.0 NULL
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
Apply a harmonic restraining force to atoms in the group to affect
|
|
their central moment about the center of mass (radius of gyration).
|
|
This fix is useful to encourage a protein or polymer to fold/unfold
|
|
and also when sampling along the radius of gyration as a reaction
|
|
coordinate (i.e. for protein folding).
|
|
|
|
The radius of gyration is defined as RG in the first formula. The
|
|
energy of the constraint and associated force on each atom is given by
|
|
the second and third formulas, when the group is at a different RG
|
|
than the target value RG0.
|
|
|
|
.. math::
|
|
|
|
{R_G}^2 & = \frac{1}{M}\sum_{i}^{N}{m_{i}\left( x_{i} -
|
|
\frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right)^{2}} \\
|
|
E & = K\left( R_G - R_{G0} \right)^{2} \\
|
|
F_{i} & = 2K\frac{m_{i}}{M}\left( 1-\frac{R_{G0}}{R_G}
|
|
\right)\left( x_{i} - \frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right)
|
|
|
|
The (:math:`x_i` - center-of-mass) term is computed taking into account
|
|
periodic boundary conditions, :math:`m_i` is the mass of the atom, and
|
|
*M* is the mass of the entire group. Note that K is thus a force constant
|
|
for the aggregate force on the group of atoms, not a per-atom force.
|
|
|
|
If :math:`R_{G0}` is specified as NULL, then the RG of the group is computed at
|
|
the time the fix is specified, and that value is used as the target.
|
|
|
|
Restart, fix_modify, output, run start/stop, minimize info
|
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
|
|
|
This fix writes the currently used reference RG (:math:`R_{G0}`) to
|
|
:doc:`binary restart files <restart>`. See the :doc:`read_restart
|
|
<read_restart>` command for info on how to re-specify a fix in an input
|
|
script that reads a restart file, so that the fix continues in an
|
|
uninterrupted fashion.
|
|
|
|
None of the :doc:`fix_modify <fix_modify>` options
|
|
are relevant to this fix.
|
|
|
|
This fix computes a global scalar which can be accessed by various
|
|
:doc:`output commands <Howto_output>`. The scalar is the reference
|
|
radius of gyration :math:`R_{G0}` used by the fix. energy change due to
|
|
this fix. The scalar value calculated by this fix is "intensive".
|
|
|
|
No parameter of this fix can be used with the *start/stop* keywords of
|
|
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
|
|
|
|
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.
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
|
|
This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS
|
|
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
|
|
|
Related commands
|
|
""""""""""""""""
|
|
|
|
:doc:`fix spring <fix_spring>`, :doc:`fix spring/self <fix_spring_self>`
|
|
:doc:`fix drag <fix_drag>`, :doc:`fix smd <fix_smd>`
|
|
|
|
Default
|
|
"""""""
|
|
|
|
none
|