From: Axel Kohlmeyer (
Date: Sun Sep 25 2016 - 23:20:00 CDT

On Sun, Sep 25, 2016 at 11:40 PM, Darren Li <> wrote:
> Hello list
> I am darren.
> When using Axel's HOOMD plugin (from VMD 1.9.2 (on 64-bit Linux,
> obtained as a binary from the VMD site) to dump xm (dump molfile command in
> lammps-30-july stable), the outcome xmls do not contain information about
> bond and angle.
> Then I use vmd to contert a pdb to hoomd xml. the outcome also misses
> bond and angle information.
> So it seems Axel's HOOMD plugin do not write topology information with
> default. Or I have wrong or missing operation?

neither pdb files, nor LAMMPS dumps contain topology information, so
they cannot be output to the hoomd file by simply writing out a HOOMD
xml file.


> Any suggestions will be appreciated.
> Thanks

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.