[lammps-users] visualization


I'm using VMD to visualize LAMMPS dumps of a system of rigid particles. Is there a way to visualize this data set such that all atoms are colored by molecular-ID?

On a semi-related note, i am able to have LAMMPS create .xtc and .dcd dump files, but after opening these files in VMD, the viewer does not show anything. However, each "molecule" i add has the correct number of atoms, however despite going through all the available representations, i cannot get anything to show up (for either dump style).

I'm running on an Macbook Pro, intel-OS X v10.5.1 machine, VMD version 1.8.6 for Mac OS X, and latest version of LAMMPS, built with the XTC package.



These are really VMD questions, so you might consider asking the VMD people.

But yes, you should be able to viz your data set such that all atoms
are colored by molecular ID. Try Graphics -> Representations ->
Coloring Method -> Molecule.

As far as dcd files go, you need to create a psf file before you can
read in a dcd file with VMD. If you have a pdb file, you can create
the psf file using psfgen (see the README file in lammps/tools/ch2lmp
). You might also consider simply having LAMMPS dump to the xyz file
format, which can be read directly by VMD.


Ah yes, Axel already actually responded to my thread on the vmd-l mailing list. The solution that i'm using is to use a custom dump style, and then use the Pizza.py toolkit to manipulate the mol-ID, convert to a pdbfile, then viz that in VMD.

Thanks for all your help!