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<title>fix tmd command — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="fix-tmd-command">
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<span id="index-0"></span><h1>fix tmd command<a class="headerlink" href="#fix-tmd-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 tmd rho_final file1 N file2
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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>tmd = style name of this fix command</li>
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<li>rho_final = desired value of rho at the end of the run (distance units)</li>
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<li>file1 = filename to read target structure from</li>
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<li>N = dump TMD statistics every this many timesteps, 0 = no dump</li>
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<li>file2 = filename to write TMD statistics to (only needed if N > 0)</li>
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</ul>
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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 1 all nve
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fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
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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>Perform targeted molecular dynamics (TMD) on a group of atoms. A
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holonomic constraint is used to force the atoms to move towards (or
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away from) the target configuration. The parameter “rho” is
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monotonically decreased (or increased) from its initial value to
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rho_final at the end of the run.</p>
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<p>Rho has distance units and is a measure of the root-mean-squared
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distance (RMSD) between the current configuration of the atoms in the
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group and the target coordinates listed in file1. Thus a value of
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rho_final = 0.0 means move the atoms all the way to the final
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structure during the course of the run.</p>
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<p>The target file1 can be ASCII text or a gzipped text file (detected by
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a .gz suffix). The format of the target file1 is as follows:</p>
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<div class="highlight-python"><div class="highlight"><pre>0.0 25.0 xlo xhi
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0.0 25.0 ylo yhi
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0.0 25.0 zlo zhi
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125 24.97311 1.69005 23.46956 0 0 -1
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126 1.94691 2.79640 1.92799 1 0 0
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127 0.15906 3.46099 0.79121 1 0 0
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...
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</pre></div>
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</div>
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<p>The first 3 lines may or may not be needed, depending on the format of
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the atoms to follow. If image flags are included with the atoms, the
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1st 3 lo/hi lines must appear in the file. If image flags are not
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included, the 1st 3 lines should not appear. The 3 lines contain the
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simulation box dimensions for the atom coordinates, in the same format
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as in a LAMMPS data file (see the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command).</p>
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<p>The remaining lines each contain an atom ID and its target x,y,z
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coordinates. The atom lines (all or none of them) can optionally be
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followed by 3 integer values: nx,ny,nz. For periodic dimensions, they
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specify which image of the box the atom is considered to be in, i.e. a
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value of N (positive or negative) means add N times the box length to
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the coordinate to get the true value.</p>
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<p>The atom lines can be listed in any order, but every atom in the group
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must be listed in the file. Atoms not in the fix group may also be
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listed; they will be ignored.</p>
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<p>TMD statistics are written to file2 every N timesteps, unless N is
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specified as 0, which means no statistics.</p>
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<p>The atoms in the fix tmd group should be integrated (via a fix nve,
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nvt, npt) along with other atoms in the system.</p>
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<p>Restarts can be used with a fix tmd command. For example, imagine a
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10000 timestep run with a rho_initial = 11 and a rho_final = 1. If a
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restart file was written after 2000 time steps, then the configuration
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in the file would have a rho value of 9. A new 8000 time step run
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could be performed with the same rho_final = 1 to complete the
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conformational change at the same transition rate. Note that for
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restarted runs, the name of the TMD statistics file should be changed
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to prevent it being overwritten.</p>
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<p>For more information about TMD, see <a class="reference internal" href="#schlitter1"><span>(Schlitter1)</span></a> and
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<a class="reference internal" href="#schlitter2"><span>(Schlitter2)</span></a>.</p>
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</div>
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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>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> 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 <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>.</p>
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<p>This fix can ramp its rho parameter over multiple runs, using the
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<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command. See the
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<a class="reference internal" href="run.html"><em>run</em></a> command for details of how to do this.</p>
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<p>This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</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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<p>All TMD fixes must be listed in the input script after all integrator
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fixes (nve, nvt, npt) are applied. This ensures that atoms are moved
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before their positions are corrected to comply with the constraint.</p>
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<p>Atoms that have a TMD fix applied should not be part of a group to
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which a SHAKE fix is applied. This is because LAMMPS assumes there
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are not multiple competing holonomic constraints applied to the same
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atoms.</p>
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<p>To read gzipped target files, you must compile LAMMPS with the
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-DLAMMPS_GZIP option - see the <a class="reference internal" href="Section_start.html#start-2"><span>Making LAMMPS</span></a> section of the documentation.</p>
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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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<hr class="docutils" />
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<p id="schlitter1"><strong>(Schlitter1)</strong> Schlitter, Swegat, Mulders, “Distance-type reaction
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coordinates for modelling activated processes”, J Molecular Modeling,
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7, 171-177 (2001).</p>
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<p id="schlitter2"><strong>(Schlitter2)</strong> Schlitter and Klahn, “The free energy of a reaction
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coordinate at multiple constraints: a concise formulation”, Molecular
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Physics, 101, 3439-3443 (2003).</p>
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