How to visualize cgdna output?

LAMMPS LAMMPS General Discussion
1

i want to visualize output from cgdna script in ChimeraX or VMD, but xtc, dcd, or lammpstrj is not enough i need a psf topology file

oxdna.in (1.7 KB)

oxdna.data (6.2 KB)

oxdna.lammpstrj (8.4 KB)

oxdna.xtc (1.8 KB)

i had a look at several places:

  1. docs.lammps.org ( no dump psf command available )

  2. CG-DNA.pdf documentation ( which mentions web-based oxview but i really want either ChimeraX or VMD which both need psf together with xtc/dcd/lamppstrj )

  3. Homepage of Axel Kohlmeyer - Various Odds & Ends ( but i the problem is “note: the atom style has to be known” and cgdna uses atom_style hybrid bond ellipsoid oxdna )

% topo readlammpsdata oxdna.lammpstrj full
Info) parsing LAMMPS header.
Warning) readlammpsheader: skipping unkown header line: 2 : 0
Warning) readlammpsheader: skipping unkown header line: 3 : ITEM: NUMBER OF ATOMS
Warning) readlammpsheader: skipping unkown header line: 4 : 15
Warning) readlammpsheader: skipping unkown header line: 5 : ITEM: BOX BOUNDS pp pp pp
Warning) readlammpsheader: skipping unkown header line: 6 : 0.0000000000000000e+00 1.0000000000000000e+02
Warning) readlammpsheader: skipping unkown header line: 7 : 0.0000000000000000e+00 1.0000000000000000e+02
Warning) readlammpsheader: skipping unkown header line: 8 : 0.0000000000000000e+00 1.0000000000000000e+02
Warning) readlammpsheader: skipping unkown header line: 9 : ITEM: ATOMS id mol type x y z ix iy iz
Warning) readlammpsheader: skipping unkown header line: 10 : 1 1 1 9.46613 17.0561 67.0815 0 0 0
Warning) readlammpsheader: skipping unkown header line: 11 : 2 1 2 9.67673 17.5086 66.8825 0 0 0
[…]
ERROR) readlammpsdata: failed to parse lammps data header. abort.

% topo readlammpsdata oxdna.lammpstrj hybrid bond ellipsoid oxdna
ERROR) Atom style ‘hybrid’ is not supported by TopoTools 1.8

  1. https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ ( but this plugin reads standard PDB files, Charmm topology files, and PSF files in X-PLOR/NAMD format )

any suggestions ? should i write a dump psf command for lammps ??

2

.lammpstrj can be used with VMD and OVITO, specifically if you use the custom style dump and use the elements property. It will be missing the bond topology, but in many cases this can be recovered by some heuristics within the visualization tool, e.g. a DynamicBonds representation in VMD.

It is also possible to try some VMD scripting using the TopoTools plugin to reconstitute the bond topology after assigning suitable covalent radii.

A dump file is not a data file. But indeed the hybrid data file is not supported (and cannot be easily supported since the data file format does not encode what the column in the Atoms section mean.

  • You should be able to write a psf file with write_dump molfile and a VMD molfile pluging for psf files, but those won’t have a bond topology either since the dump molfile procedure does not support that.
  • dump psf does not make much sense, since the psf file does not contain coordinate information, a write_psf command would be more appropriate. It would be most useful in combination with type labels (a rather new feature) which would contain the force field type information required for the psf file.