msi2lmp
@@ -189,6 +190,21 @@
+lmp2vmd tool
+
+The lmp2vmd sub-directory contains some scripts for converting LAMMPS
+files into formats suitable for visualizing with the VMD
+package.
+
+One script extracts bond topology info from a LAMMPS data file. A
+second script attached amino acid (residue) information to what is
+extracted from a data file. See the README file for more information.
+
+These scripts were written by Axel Kohlmeyer (akohlmey at
+cmm.chem.upenn.edu) at U Penn.
+
+
+
matlab tool
The matlab sub-directory contains several MATLAB scripts for
diff -Naur lammps-28Mar08/doc/Section_tools.txt lammps-30Mar08/doc/Section_tools.txt
--- lammps-28Mar08/doc/Section_tools.txt 2008-03-18 14:18:54.000000000 -0600
+++ lammps-30Mar08/doc/Section_tools.txt 2008-03-28 09:03:22.000000000 -0600
@@ -48,6 +48,7 @@
"lmp2arc"_#arc
"lmp2cfg"_#cfg
"lmp2traj"_#traj
+"lmp2vmd"_#vmd
"matlab"_#matlab
"micelle2d"_#micelle
"msi2lmp"_#msi
@@ -185,6 +186,21 @@
:line
+lmp2vmd tool :h4,link(vmd)
+
+The lmp2vmd sub-directory contains some scripts for converting LAMMPS
+files into formats suitable for visualizing with the "VMD
+package"_http://www.ks.uiuc.edu/Research/vmd/.
+
+One script extracts bond topology info from a LAMMPS data file. A
+second script attached amino acid (residue) information to what is
+extracted from a data file. See the README file for more information.
+
+These scripts were written by Axel Kohlmeyer (akohlmey at
+cmm.chem.upenn.edu) at U Penn.
+
+:line
+
matlab tool :h4,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlab scripts for
diff -Naur lammps-28Mar08/tools/lmp2vmd/README lammps-30Mar08/tools/lmp2vmd/README
--- lammps-28Mar08/tools/lmp2vmd/README 1969-12-31 17:00:00.000000000 -0700
+++ lammps-30Mar08/tools/lmp2vmd/README 2008-03-28 09:02:29.000000000 -0600
@@ -0,0 +1,109 @@
+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
+.
+
+-------------------------
+
+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
+
+-------------------------
+
+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
+
+
diff -Naur lammps-28Mar08/tools/lmp2vmd/lmpbonds2vmd.tcl lammps-30Mar08/tools/lmp2vmd/lmpbonds2vmd.tcl
--- lammps-28Mar08/tools/lmp2vmd/lmpbonds2vmd.tcl 1969-12-31 17:00:00.000000000 -0700
+++ lammps-30Mar08/tools/lmp2vmd/lmpbonds2vmd.tcl 2008-03-28 09:02:29.000000000 -0600
@@ -0,0 +1,56 @@
+# small script to extract bonding info from a lammps data file
+# so that VMD will display the correct bonds for CG-MD.
+# (c) 2007 Axel Kohlmeyer
+
+proc lmpbondsfromdata {mol filename} {
+
+ # create an empty bondlist
+ set na [molinfo $mol get numatoms]; # number of atoms
+ set nb 0; # number of bonds
+ set bl {}; # bond list
+ for {set i 0} {$i < $na} {incr i} {
+ lappend bl {}
+ }
+
+ # open lammps data file
+ if {[catch {open $filename r} fp]} {
+ puts stderr "could not open file $filename"
+ return -1
+ }
+
+ # read file line by line until we hit the Bonds keyword
+ while {[gets $fp line] >= 0} {
+ # pick number of bonds
+ regexp {^\s*(\d+)\s+bonds} $line dummy nb
+
+ if { [regexp {^\s*Bonds} $line] } {
+ puts "nbonds= $nb\n now reading Bonds section"
+ break
+ }
+ }
+
+ # skip one line
+ gets $fp line
+ # read the bonds file
+ for {set i 0} {$i < $nb} {incr i} {
+ gets $fp line
+ # grep bond numbers from entry and adjust to VMD numbering style
+ regexp {^\s*\d+\s+\d+\s+(\d+)\s+(\d+)} $line dummy ba bb
+ incr ba -1
+ incr bb -1
+
+ set bn [lindex $bl $ba]
+ lappend bn $bb
+ set bl [lreplace $bl $ba $ba $bn]
+
+ set bn [lindex $bl $bb]
+ lappend bn $ba
+ set bl [lreplace $bl $bb $bb $bn]
+ }
+ close $fp
+
+ set sel [atomselect $mol all]
+ $sel setbonds $bl
+ $sel delete
+}
+
diff -Naur lammps-28Mar08/tools/lmp2vmd/lmpresid2vmd.tcl lammps-30Mar08/tools/lmp2vmd/lmpresid2vmd.tcl
--- lammps-28Mar08/tools/lmp2vmd/lmpresid2vmd.tcl 1969-12-31 17:00:00.000000000 -0700
+++ lammps-30Mar08/tools/lmp2vmd/lmpresid2vmd.tcl 2008-03-28 09:02:29.000000000 -0600
@@ -0,0 +1,47 @@
+# small script to extract residue info from a lammps data file
+# (c) 2008 Axel Kohlmeyer
+
+proc lmpresidfromdata {mol filename} {
+
+ # create an empty bondlist
+ set na [molinfo $mol get numatoms]; # number of atoms of molecule
+ set nb 0; # number of atoms in data file
+ set bl {}; # resid list
+ for {set i 0} {$i < $na} {incr i} {
+ lappend bl 0
+ }
+
+ # open lammps data file
+ if {[catch {open $filename r} fp]} {
+ puts stderr "could not open file $filename"
+ return -1
+ }
+
+ # read file line by line until we hit the Bonds keyword
+ while {[gets $fp line] >= 0} {
+ # pick number of bonds
+ regexp {^\s*(\d+)\s+atoms} $line dummy nb
+
+ if { [regexp {^\s*Atoms} $line] } {
+ puts "atoms= $nb\n now reading Atoms section"
+ break
+ }
+ }
+
+ # skip one line
+ gets $fp line
+ # read the Atoms data
+ for {set i 0} {$i < $nb} {incr i} {
+ gets $fp line
+ # grep bond numbers from entry and adjust to VMD numbering style
+ regexp {^\s*(\d+)\s+(\d+)\s+\d+.*} $line dummy ba bb
+ incr ba -1
+ lset bl $ba $bb
+ }
+ close $fp
+
+ set sel [atomselect $mol all]
+ $sel set resid $bl
+ $sel delete
+}
+