VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Sep 25 2016 - 23:20:00 CDT

• Next message: Darren Li: "Q=BD=AC=E5=8F=91=EF=BC=9A__by_using_Ax?= el's HOOMD plugin, convert pdb to xml and missing bond information"
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On Sun, Sep 25, 2016 at 11:40 PM, Darren Li <shujiajlu_at_remove_yahoo.com> 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.

axel.

> Any suggestions will be appreciated.
>
> Thanks
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

• Next message: Darren Li: "Q=BD=AC=E5=8F=91=EF=BC=9A__by_using_Ax?= el's HOOMD plugin, convert pdb to xml and missing bond information"
• Previous message: Darren Li: "by using Axel's HOOMD plugin, convert pdb to xml and missing bond information"
• In reply to: Darren Li: "by using Axel's HOOMD plugin, convert pdb to xml and missing bond information"
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