From: Darren Li (
Date: Sun Sep 25 2016 - 22:40:02 CDT

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?    Any suggestions will be appreciated.