Various Odds & Ends

In most visualization programs specific colors are associated with specific elements. However in a LAMMPS data file that atoms are only identified by their type and thus the embedded data file reader in the topotools package imports those as atom names (unless a very special extended data file syntax is used). The TopoTools plugin has some utilities to help with this process and other VMD script commands can be used to help as well. However, it is important to note that this process can it automated form only recover information that is present in the data. Since the generation of a data file usually means that unneeded information is lost, further reconstruction requires additional knowledge about the system in the data file. The first example discusses the reconstruction of a .psf/.pdb file for a bulk HDPE data file, data.hdpe-x5 using the script reconstructhdpe.tcl.The process starts with reading in the data file (note: the atom style has to be known):

topo readlammpsdata data.hdpe-x5 full

With this information loaded, we would get a visualization like in the left side of the image. Now we can try to guess the element names from the atomic masses and use those to set other properties like atom name or radius. Of course, this step only works, if the masses are actually given in the data file:

topo guessatom element mass

topo guessatom name element

topo guessatom radius element

Based on the element name and further knowledge about the system, we can set a few more properties, that help with analysis or visualization:

set selc [atomselect top {name C}]

$selc set type CT

$selc set resname HDPE

# set residue ID to a 1-based index.

set resid {}

foreach r [$selc get residue] { incr r; lappend resid $r }

$selc set resid $resid

The similar process is performed for all hydrogens. We can then add further cleanups, e.g. retyping of bonds or angles. One very special operation would be the clearing of all defined improper dihedrals, since a look at the embedded coefficient shows that those are all zero. This done via:

topo clearimpropers

Finally we let VMD reanalyze the molecular information and write out the information in the desired formats:

mol reanalyze top

animate write psf hdpe-x5.psf

animate write pdb hdpe-x5.pdb

For a single-walled carbon nanotube (data.swcnt-5,5) we could perform the same operation, but in this case, we need to keep impropers and would benefit from setting a different atom type (for aromatic carbons) as shown in the script reconstructswcnt.tcl.