VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 26 2016 - 06:11:58 CDT

On Mon, Sep 26, 2016 at 2:45 AM, Darren Li <shujiajlu_at_remove_yahoo.com> wrote:
>
>
> 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.

as i mentioned, pdb files do not contain topology information.

>
> //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?

no.

> I find the dump_molfile.cpp written by you.
> http://www.cfm.brown.edu/repo/release/USER-MESO/USER-MOLFILE/dump_molfile.cpp
> It 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
> yes
> or
> dump 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?

these flags have never been implemented.

the route to obtain topology information from LAMMPS is to
read/process a data file.
however, that is not a fully automatic procedure, since LAMMPS data
files usually do not contain the necessary meta-data for it.

axel.

>
> 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.
>
>
>
>
> 

-- 
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.