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<li>fix restrain command</li>
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<div itemprop="articleBody">
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<div class="section" id="fix-restrain-command">
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<span id="index-0"></span><h1>fix restrain command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">restrain</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
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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"><span class="doc">fix</span></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</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">holdem</span> <span class="nb">all</span> <span class="n">restrain</span> <span class="n">bond</span> <span class="mi">45</span> <span class="mi">48</span> <span class="mf">2000.0</span> <span class="mf">2000.0</span> <span class="mf">2.75</span>
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<span class="n">fix</span> <span class="n">holdem</span> <span class="nb">all</span> <span class="n">restrain</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mf">2000.0</span> <span class="mf">2000.0</span> <span class="mf">120.0</span>
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<span class="n">fix</span> <span class="n">holdem</span> <span class="nb">all</span> <span class="n">restrain</span> <span class="n">bond</span> <span class="mi">45</span> <span class="mi">48</span> <span class="mf">2000.0</span> <span class="mf">2000.0</span> <span class="mf">2.75</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mf">2000.0</span> <span class="mf">2000.0</span> <span class="mf">120.0</span>
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<span class="n">fix</span> <span class="n">texas_holdem</span> <span class="nb">all</span> <span class="n">restrain</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mf">0.0</span> <span class="mf">2000.0</span> <span class="mf">120.0</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">5</span> <span class="mf">0.0</span> <span class="mf">2000.0</span> <span class="o">-</span><span class="mf">120.0</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">6</span> <span class="mf">0.0</span> <span class="mf">2000.0</span> <span class="mf">0.0</span>
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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</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"><span class="doc">read_data</span></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"><span class="doc">run</span></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"><span class="doc">minimize</span></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-default"><div class="highlight"><pre><span></span># 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"><span class="doc">bond_style harmonic</span></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"><span class="doc">angle_style harmonic</span></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"><span class="doc">dihedral_style charmm</span></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</h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></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"><span class="doc">thermodynamic output</span></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"><span class="doc">fix_modify</span></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 class="std std-ref">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"><span class="doc">run</span></a> command.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</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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</div>
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</div>
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</div>
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</div>
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<footer>
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<hr/>
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<div role="contentinfo">
|
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<p>
|
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© Copyright 2013 Sandia Corporation.
|
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</p>
|
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</div>
|
||
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|
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|
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</footer>
|
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</div>
|
||
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</div>
|
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</section>
|
||
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</div>
|
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|
||
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|
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|
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<script type="text/javascript">
|
||
|
|
var DOCUMENTATION_OPTIONS = {
|
||
|
|
URL_ROOT:'./',
|
||
|
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VERSION:'',
|
||
|
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COLLAPSE_INDEX:false,
|
||
|
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FILE_SUFFIX:'.html',
|
||
|
|
HAS_SOURCE: true
|
||
|
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};
|
||
|
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</script>
|
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<script type="text/javascript" src="_static/jquery.js"></script>
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<script type="text/javascript" src="_static/underscore.js"></script>
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