83 lines
2.7 KiB
ReStructuredText
83 lines
2.7 KiB
ReStructuredText
.. index:: fix spring/rg
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fix spring/rg 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 spring/rg K RG0
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* spring/rg = style name of this fix command
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* K = harmonic force constant (force/distance units)
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* RG0 = target radius of gyration to constrain to (distance units)
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.. parsed-literal::
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if RG0 = NULL, use the current RG as the target value
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 protein spring/rg 5.0 10.0
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fix 2 micelle spring/rg 5.0 NULL
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Description
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"""""""""""
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Apply a harmonic restraining force to atoms in the group to affect
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their central moment about the center of mass (radius of gyration).
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This fix is useful to encourage a protein or polymer to fold/unfold
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and also when sampling along the radius of gyration as a reaction
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coordinate (i.e. for protein folding).
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The radius of gyration is defined as RG in the first formula. The
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energy of the constraint and associated force on each atom is given by
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the second and third formulas, when the group is at a different RG
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than the target value RG0.
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.. math::
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{R_G}^2 & = \frac{1}{M}\sum_{i}^{N}{m_{i}\left( x_{i} -
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\frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right)^{2}} \\
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E & = K\left( R_G - R_{G0} \right)^{2} \\
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F_{i} & = 2K\frac{m_{i}}{M}\left( 1-\frac{R_{G0}}{R_G}
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\right)\left( x_{i} - \frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right)
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The (:math:`x_i` - center-of-mass) term is computed taking into account
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periodic boundary conditions, :math:`m_i` is the mass of the atom, and
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*M* is the mass of the entire group. Note that K is thus a force constant
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for the aggregate force on the group of atoms, not a per-atom force.
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If :math:`R_{G0}` is specified as NULL, then the RG of the group is computed at
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the time the fix is specified, and that value is used as the target.
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**Restart, fix_modify, output, run start/stop, minimize info:**
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various :doc:`output commands <Howto_output>`.
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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. This fix is not invoked during :doc:`energy minimization <minimize>`.
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The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
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fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
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integrator the fix is adding its forces. Default is the outermost level.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`fix spring <fix_spring>`, :doc:`fix spring/self <fix_spring_self>`
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:doc:`fix drag <fix_drag>`, :doc:`fix smd <fix_smd>`
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**Default:** none
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