lammps/tools/lmp2vmd

This directory contains utility scripts for using VMD to visualize and
analyze LAMMPS trajectories (well, right now there is only two
scripts, but more are to come). Below are short descriptions and
examples on how to use them. Additional information on VMD as well as
additional scripts can be found at:
http://www.ks.uiuc.edu/Research/vmd/

The scripts here are maintained by Axel Kohlmeyer
<akohlmey@cmm.chem.upenn.edu>.

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1. lmpbonds2vmd.tcl - translate bonding information from a LAMMPS data
   file into VMD.

1a. Background.
   With VMD one typically reads bonding information from a topology file and 
   then reads a trajectory with the coordinate information on top of that.
   The most common use is the combination of a (CHARMM or X-PLOR style) .psf
   file and a .dcd file. If the bonding information is not avaiable, VMD uses
   a heuristic guess, which does not always work, but can be particularly
   cumbersome in coarse grained MD or similar systems. The lmpbonds2vmd.tcl
   script provide an option to transfer bonding information from a LAMMPS data
   file into VMD.

1b. Usage 
   The script defines a new procedure "lmpbondsfromdata". To activate it
   type at the VMD command prompt:

   source lmpbonds2vmd.tcl

   To then build a .psf file that can be used for subsequent
   visualizations you can load one frame of a native LAMMPS trajectory
   (not binary, not custom!), e.g. perusing the output from the
   micelle example.

   mol new dump.micelle type lammpstrj waitfor all
   lmpbondsfromdata 0 data.micelle

   now you should only see the bonds that actually have bonded interactions.

   to avoid having to run the script all the time you can save the bonding 
   information in an (incomplete) .psf file.

   animate write psf micelle.psf

   and now in the future you can load this psf file first and then 
   the dump file (or a more compact and faster loading .dcd or .xtc file).
   e.g., with:

   vmd micelle.psf -lammpstrj dump.micelle

1c. Problems
   The data file format is quite flexible and thus not always easy to parse
   independent from context. As a consequence, the lmpbondsfromdata parser
   may be confused by your specific setup.

1d. History
   First version. 2007, axel kohlmeyer <akohlmey@cmm.chem.upenn.edu>

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2. lmpresid2vmd.tcl - translate residue information from a LAMMPS data
   file into VMD.

2a Background.  LAMMPS dump files contain information about the
   (numerical) atom type, but not a molecule or residue id as it is
   typically used in .psf or .pdf files to define subunits of a
   system. Adding this information can be very helpful for analysis
   and postprocessing of LAMMPS data in VMD.

2b Usage.
   The script defines a new procedure "lmpresidfromdata". To activate it
   type at the VMD command prompt:

   source lmpresid2vmd.tcl

   To then add the residue information to a .psf file, see the steps for from
   item 1 from above and then type into the VMD console.
   
   lmpresidfromdata 0 data.micelle

   to avoid having to run the script all the time you can save the bonding
   information in an (incomplete) .psf file.

   animate write psf micelle2.psf

   and now in the future you can load this psf file first and then
   the dump file (or a more compact and faster loading .dcd or .xtc file).
   e.g., with:

   vmd micelle2.psf -lammpstrj dump.micelle

   now you can use the residue information to "join" the bonds split
   across the periodic boundaries with:

   pbc join residue -all

   and then enjoy a nice visualization of the micelle example with VMD. :)

2c. Problems
   The data file format is quite flexible and thus not always easy to parse
   independent from context. As a consequence, the lmpresidfromdata parser
   may be confused by your specific setup.

2d. History
   First version. 2008, axel kohlmeyer <akohlmey@cmm.chem.upenn.edu>