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.

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

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.

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

(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.

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. :)

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.

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