2006-09-22 00:22:34 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>fix tmd command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID tmd rho_final file1 N file2
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>tmd = style name of this fix command
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<LI>rho_final = desired value of rho at the end of the run (distance units)
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<LI>file1 = filename to read target structure from
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<LI>N = dump TMD statistics every this many timesteps, 0 = no dump
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<LI>file2 = filename to write TMD statistics to (only needed if N > 0)
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</UL>
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<P><B>Examples:</B>
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</P>
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<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>
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<P><B>Description:</B>
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</P>
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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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2007-06-26 08:03:39 +08:00
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rho_final at the end of the run.
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2006-09-22 00:22:34 +08:00
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</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.
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</P>
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2008-01-18 07:46:30 +08:00
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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:
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2006-09-22 00:22:34 +08:00
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</P>
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<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>
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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 HREF = "read_data.html">read_data</A> command).
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</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.
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</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.
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</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.
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</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.
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</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.
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</P>
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<P>For more information about TMD, see <A HREF = "#Schlitter1">(Schlitter1)</A> and
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<A HREF = "#Schlitter2">(Schlitter2)</A>.
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</P>
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2007-10-11 06:28:11 +08:00
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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2010-04-03 00:51:06 +08:00
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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 HREF = "Section_howto.html#4_15">output
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2007-10-11 06:28:11 +08:00
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commands</A>.
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2007-06-26 08:03:39 +08:00
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</P>
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<P>This fix can ramp its rho parameter over multiple runs, using the
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<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
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<A HREF = "run.html">run</A> command for details of how to do this.
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</P>
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<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Restrictions:</B>
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</P>
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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.
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</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.
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</P>
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2008-01-18 07:46:30 +08:00
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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 HREF = "Section_start.html#2_2">Making LAMMPS</A>
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section of the documentation.
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Schlitter1"></A>
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<P><B>(Schlitter1)</B> 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).
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</P>
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<A NAME = "Schlitter2"></A>
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<P><B>(Schlitter2)</B> 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).
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</P>
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</HTML>
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