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<div class="section" id="fix-restrain-command">
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<span id="index-0"></span><h1>fix restrain command<a class="headerlink" href="#fix-restrain-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID restrain keyword args ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>restrain = style name of this fix command</li>
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<li>one or more keyword/arg pairs may be appended</li>
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<li>keyword = <em>bond</em> or <em>angle</em> or <em>dihedral</em></li>
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</ul>
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<pre class="literal-block">
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<em>bond</em> 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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<em>angle</em> 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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<em>dihedral</em> 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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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>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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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>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 <a class="reference internal" href="read_data.html"><em>read_data</em></a> 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.</p>
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<p>The group-ID specified by this fix is ignored.</p>
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<p>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.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">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 <a class="reference internal" href="run.html"><em>run</em></a> 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 <a class="reference internal" href="minimize.html"><em>minimize</em></a> 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).</p>
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</div>
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<p>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.</p>
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<p>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:</p>
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<div class="highlight-python"><div class="highlight"><pre># 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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</pre></div>
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</div>
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<hr class="docutils" />
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<p>The <em>bond</em> keyword applies a bond restraint to the specified atoms
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using the same functional form used by the <a class="reference internal" href="bond_harmonic.html"><em>bond_style harmonic</em></a> command. The potential associated with
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the restraint is</p>
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<img alt="_images/bond_harmonic.jpg" class="align-center" src="_images/bond_harmonic.jpg" />
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<p>with the following coefficients:</p>
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<ul class="simple">
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<li>K (energy/distance^2)</li>
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<li>r0 (distance)</li>
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</ul>
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<p>K and r0 are specified with the fix. Note that the usual 1/2 factor
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is included in K.</p>
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<hr class="docutils" />
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<p>The <em>angle</em> keyword applies an angle restraint to the specified atoms
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using the same functional form used by the <a class="reference internal" href="angle_harmonic.html"><em>angle_style harmonic</em></a> command. The potential associated with
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the restraint is</p>
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<img alt="_images/angle_harmonic.jpg" class="align-center" src="_images/angle_harmonic.jpg" />
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<p>with the following coefficients:</p>
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<ul class="simple">
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<li>K (energy/radian^2)</li>
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<li>theta0 (degrees)</li>
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</ul>
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<p>K and theta0 are specified with the fix. Note that the usual 1/2
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factor is included in K.</p>
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<hr class="docutils" />
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<p>The <em>dihedral</em> 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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<a class="reference internal" href="dihedral_charmm.html"><em>dihedral_style charmm</em></a> command. The potential
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associated with the restraint is</p>
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<img alt="_images/dihedral_charmm.jpg" class="align-center" src="_images/dihedral_charmm.jpg" />
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<p>with the following coefficients:</p>
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<ul class="simple">
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<li>K (energy)</li>
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<li>n = 1</li>
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<li>d (degrees) = phi0 + 180</li>
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</ul>
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<p>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.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> 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 <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">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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<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option for this fix.</p>
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</div>
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<p>This fix computes a global scalar, which can be accessed by various
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<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. 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”.</p>
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<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
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the <a class="reference internal" href="run.html"><em>run</em></a> command.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<blockquote>
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<div>none</div></blockquote>
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<p><strong>Related commands:</strong> none</p>
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<p><strong>Default:</strong> none</p>
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