git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14950 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/_sources/fix_tmd.txt

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+.. index:: fix tmd
+
+fix tmd command
+===============
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID tmd rho_final file1 N file2
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* tmd = style name of this fix command
+* rho_final = desired value of rho at the end of the run (distance units)
+* file1 = filename to read target structure from
+* N = dump TMD statistics every this many timesteps, 0 = no dump
+* file2 = filename to write TMD statistics to (only needed if N > 0)
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   fix 1 all nve
+   fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file
+
+Description
+"""""""""""
+
+Perform targeted molecular dynamics (TMD) on a group of atoms.  A
+holonomic constraint is used to force the atoms to move towards (or
+away from) the target configuration.  The parameter "rho" is
+monotonically decreased (or increased) from its initial value to
+rho_final at the end of the run.
+
+Rho has distance units and is a measure of the root-mean-squared
+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
+structure during the course of the run.
+
+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:
+
+.. parsed-literal::
+
+   0.0 25.0 xlo xhi
+   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
+   ...
+
+The first 3 lines may or may not be needed, depending on the format of
+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
+as in a LAMMPS data file (see the :doc:`read_data <read_data>` command).
+
+The remaining lines each contain an atom ID and its target x,y,z
+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
+the coordinate to get the true value.
+
+The atom lines can be listed in any order, but every atom in the group
+must be listed in the file.  Atoms not in the fix group may also be
+listed; they will be ignored.
+
+TMD statistics are written to file2 every N timesteps, unless N is
+specified as 0, which means no statistics.
+
+The atoms in the fix tmd group should be integrated (via a fix nve,
+nvt, npt) along with other atoms in the system.
+
+Restarts can be used with a fix tmd command.  For example, imagine a
+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
+to prevent it being overwritten.
+
+For more information about TMD, see :ref:`(Schlitter1) <Schlitter1>` and
+:ref:`(Schlitter2) <Schlitter2>`.
+
+Restart, fix_modify, output, run start/stop, minimize info
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various :ref:`output commands <howto_15>`.
+
+This fix can ramp its rho parameter over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+
+All TMD fixes must be listed in the input script after all integrator
+fixes (nve, nvt, npt) are applied.  This ensures that atoms are moved
+before their positions are corrected to comply with the constraint.
+
+Atoms that have a TMD fix applied should not be part of a group to
+which a SHAKE fix is applied.  This is because LAMMPS assumes there
+are not multiple competing holonomic constraints applied to the same
+atoms.
+
+To read gzipped target files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the :ref:`Making LAMMPS <start_2>` section of the documentation.
+
+**Related commands:** none
+
+**Default:** none
+
+
+----------
+
+
+.. _Schlitter1:
+
+
+
+**(Schlitter1)** Schlitter, Swegat, Mulders, "Distance-type reaction
+coordinates for modelling activated processes", J Molecular Modeling,
+7, 171-177 (2001).
+
+.. _Schlitter2:
+
+
+
+**(Schlitter2)** Schlitter and Klahn, "The free energy of a reaction
+coordinate at multiple constraints: a concise formulation", Molecular
+Physics, 101, 3439-3443 (2003).
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm