VMD-L Mailing List

From: Darren Li (shujiajlu_at_REMOVE_yahoo.com)
Date: Mon Sep 26 2016 - 01:45:01 CDT

     Darren Li <shujiajlu_at_yahoo.com> 于 2016年9月26日, 星期一, 下午 2:38 写道：
 

 Thank you for your time and help.
I have just tried to convet xml to xml through vmd. The plugin works and do not lose information. Sorry for not testing enough.   "vmd -pdb *.pdb"  can  show bond structure, but  at last I found that it is from "determining bond structure from distance search" and is wrong.

//The follows are about lammps. It is OK if you choose to ignore them.
You mean that "dump molfile" can not output topology information? Is there any other way to write out hoomd xml containing topology information when using  lammps?I find the dump_molfile.cpp written by you.  http://www.cfm.brown.edu/repo/release/USER-MESO/USER-MOLFILE/dump_molfile.cppIt contains:
// syntax:
// dump <id> <groupid> molfile <every> <filename> <type> [<path>]
// path defaults to "." -> will look for .so files in CWD.
//
// XXX: potential change: add more options and make them optional
// path <path>
// template <file> <type> (import name and topology information from file)
// bonds <yes|no> (write out bond information)
// topology <yes|no> (write out all topology information)dump 1 all molfile 1000 melt.*.xml hoomd  ~/vmd/lib/vmd/plugins/LINUXAMD64/molfile template data.979000 bonds bonds yesordump 1 all molfile 1000 melt.*.xml hoomd  ~/vmd/lib/vmd/plugins/LINUXAMD64/molfile template restart.xml bonds bonds yes
//restart.xml is a typical hoomd blue xml.  data.979000 is a typical  lammps data file.
lammps does not report any error. However, the output xml still does not contain bonds information. Dose my syntax is wrong. Or this way is by no means working?

Darren

 

    Axel Kohlmeyer <akohlmey_at_gmail.com> 于 2016年9月26日, 星期一, 下午 12:20 写道：
 

 

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.