VMD-L Mailing List
From: Darren Li (shujiajlu_at_REMOVE_yahoo.com)
Date: Sun Sep 25 2016 - 22:40:02 CDT
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.