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< title > fix tmd command — LAMMPS documentation< / title >
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< li > fix tmd command< / li >
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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 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix ID group-ID tmd rho_final file1 N file2
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > command< / li >
< li > tmd = style name of this fix command< / li >
< li > rho_final = desired value of rho at the end of the run (distance units)< / li >
< li > file1 = filename to read target structure from< / li >
< li > N = dump TMD statistics every this many timesteps, 0 = no dump< / li >
< li > file2 = filename to write TMD statistics to (only needed if N > 0)< / li >
< / ul >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix 1 all nve
fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< 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 >
< 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
group and the target coordinates listed in file1. Thus a value of
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 >
< p > The target file1 can be ASCII text or a gzipped text file (detected by
a .gz suffix). The format of the target file1 is as follows:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > 0.0 25.0 xlo xhi
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0.0 25.0 ylo yhi
0.0 25.0 zlo zhi
125 24.97311 1.69005 23.46956 0 0 -1
126 1.94691 2.79640 1.92799 1 0 0
127 0.15906 3.46099 0.79121 1 0 0
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...
< / pre > < / div >
< / div >
< 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
1st 3 lo/hi lines must appear in the file. If image flags are not
included, the 1st 3 lines should not appear. The 3 lines contain the
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 >
< 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
followed by 3 integer values: nx,ny,nz. For periodic dimensions, they
specify which image of the box the atom is considered to be in, i.e. a
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 >
< 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 >
< p > TMD statistics are written to file2 every N timesteps, unless N is
specified as 0, which means no statistics.< / p >
< p > The atoms in the fix tmd group should be integrated (via a fix nve,
nvt, npt) along with other atoms in the system.< / p >
< 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
restart file was written after 2000 time steps, then the configuration
in the file would have a rho value of 9. A new 8000 time step run
could be performed with the same rho_final = 1 to complete the
conformational change at the same transition rate. Note that for
restarted runs, the name of the TMD statistics file should be changed
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to prevent it being overwritten.< / p >
< p > For more information about TMD, see < a class = "reference internal" href = "#schlitter1" > < span > (Schlitter1)< / span > < / a > and
< a class = "reference internal" href = "#schlitter2" > < span > (Schlitter2)< / span > < / a > .< / p >
< / div >
< div class = "section" id = "restart-fix-modify-output-run-start-stop-minimize-info" >
< 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 >
< 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 >
< p > This fix can ramp its rho parameter over multiple runs, using the
< em > start< / em > and < em > stop< / em > keywords of the < a class = "reference internal" href = "run.html" > < em > run< / em > < / a > command. See the
< a class = "reference internal" href = "run.html" > < em > run< / em > < / a > command for details of how to do this.< / p >
< p > This fix is not invoked during < a class = "reference internal" href = "minimize.html" > < em > energy minimization< / em > < / a > .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< 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 >
< 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
are not multiple competing holonomic constraints applied to the same
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atoms.< / p >
< p > To read gzipped target files, you must compile LAMMPS with the
-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 >
< p > < strong > Related commands:< / strong > none< / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "schlitter1" > < strong > (Schlitter1)< / strong > Schlitter, Swegat, Mulders, “ Distance-type reaction
coordinates for modelling activated processes” , J Molecular Modeling,
7, 171-177 (2001).< / p >
< p id = "schlitter2" > < strong > (Schlitter2)< / strong > Schlitter and Klahn, “ The free energy of a reaction
coordinate at multiple constraints: a concise formulation” , Molecular
Physics, 101, 3439-3443 (2003).< / p >
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