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This directory contains utility scripts for using VMD to visualize and analyze
LAMMPS trajectories (hopefully in the future this will turn into a plugin or
proper library). 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/
and: http://www.theochem.rub.de/go/cpmd-vmd.html
The scripts are maintained by Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>;
please contact him through the LAMMPS mailing list in case of problems.
-------------------------
0. Installation.
The scripts below define new tcl procedures for use with the tcl script
interpreter embedded into VMD. To activate them, you can load them by using
the "source" command. However it is more convenient to have VMD load them
automatically on demand. To do this, you need to modify your .vmdrc (or
vmd.rc) file (see the VMD User's Guide for details) and add the and adapted
version of the following code.
# add local (auto-loaded) scripts to the interpreter search path
set auto_path [concat $env(HOME)/lammps/tools/lmp2vmd $auto_path]
With this change the "source" command lines below are no longer needed. If
you add new files or procedures to this directory, you have to run the
mkindex script to update the tclIndex file.
-------------------------
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 (the latter can be produced by LAMMPS directly). If the
bonding information is not available, VMD uses a heuristic guess which
works reasonably well with biological systems, but can be particularly
cumbersome in coarse grained MD or similar model systems. The
lmpbonds2vmd.tcl script provides 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 for use in subsequent visualizations you can load
one just frame of a native LAMMPS trajectory (not binary, not custom!), for
example perusing the output from the micelle example.
mol new dump.micelle type lammpstrj waitfor all
lmpbondsfromdata [molinfo top] 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
In the future you can now load this PSF file first and then the LAMMPS dump
file(s) (or a more compact and faster loading DCD or XTC file) with:
vmd micelle.psf -lammpstrj dump.micelle
1c. Problems.
The LAMMPS data file format is quite flexible and thus not always easy to
parse independently 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>
Added a sanity check 03/2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
-------------------------
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 PDB files
to define subunits of a system. Adding this information can be very helpful
for analysis and post-processing 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 [molinfo top] data.micelle
To avoid having to run the script all the time you can save the residue
information in an (incomplete) PSF file.
animate write psf micelle2.psf
In the future you can now load this PSF file first and then the LAMMPS dump
file(s) (or a more compact and faster loading DCD or XTC file) with:
vmd micelle2.psf -lammpstrj dump.micelle
You can use the residue information to join 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 LAMMPS 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>
-------------------------
3. lmpname2vmd.tcl - set atom names based on LAMMPS type in VMD.
3a. Background.
LAMMPS dump files contain information about the (numerical) atom type, but
not atom names like in PSF or PDB files. The names are used in VMD to guess
element, radius and (default) coloring. Adding this information can be very
helpful to set convenient defaults for visualization of LAMMPS data in VMD.
3b. Usage.
The script defines a new procedure "lmptypetoname". To activate it type
at the VMD command prompt:
source lmpname2vmd.tcl
To then add atom name information, e.g., to a PSF file, see the steps for
item 1 from above and then type into the VMD console.
lmptypetoname [molinfo top] "SOL HDR TL1 TL2"
To avoid having to run the script all the time you can save the bonding
information in an (incomplete) PSF file.
animate write psf micelle3.psf
In the future you can now load this PSF file first and then the LAMMPS dump
file(s) (or a more compact and faster loading DCD or XTC file) with:
vmd micelle3.psf -lammpstrj dump.micelle
And you'll see that VMD will assign different colors to the atom types. You
cat get the previous coloring back by using the "Type" coloring scheme.
3c. Problems.
This script assumes the data originates from a LAMMPS dump file and thus
the atoms types are numerical starting from 1. If those have been modified
by some means, no name will be assigned.
3d. History.
First version. 2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
-------------------------
4. lmpradius2vmd.tcl - set VdW radius based on LAMMPS type in VMD.
4a. Background.
The radii used for VDW and derived representations in VMD are guessed from
the atom names. This script offers a convenient way to reset them (e.g. by
using the sigma parameters from matching LJ interactions).
4b. Usage.
The script defines a new procedure "lmptypetoradius". To activate it type
at the VMD command prompt:
source lmpradius2vmd.tcl
To then add atom radius information, see the steps for
item 1 from above and then type into the VMD console.
lmptypetoradius [molinfo top] "1.00 1.00 0.75 0.50"
4c. Problems.
This script assumes the data originates from a LAMMPS dump file and thus
the atoms types are numerical starting from 1. If those have been modified
by some means, no name will be assigned. There is currently no file format
that exports the radius information, so this script/command has to be
added, e.g., to "saved states" and other visualization scripts.
4d. History.
First version. 2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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