VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 19 2016 - 15:38:21 CDT

On Tue, Apr 19, 2016 at 4:05 PM, 王妙郡 <flsorrow_at_gmail.com> wrote:

> Dear users,
>
> I attend a problem while writing out the data file from VMD. I have 4 bond
> types and 5 angle types during simulation; however, when I try to output my
> data using "topo writedatafile" from VMD, the data file shows that I only
> have 1 bond type and 1 angle type. I think that write_data command in
> LAMMPS can solve this problem, but I am curious why this is happening in
> VMD . Also, is there any way to solve this problem by using VMD?
>

from your description ​it is not clear which files in which formats you are
read​ing into VMD and what you do in between. also, it is crucially
important that you let us know which version of VMD exactly and
particularly which version of the topotools plugin you are using. if you
are not using the latest version of each, you may be missing features or
there may be bugs that have been corrected since.

that said, topotools can only output information that is present in VMD.
most trajectory file formats do not provide topology information and also
some topology file format, e.g. psf do not contain any type information
outside of atom types. so unless you are using a suitable process of
reading the complete information or reconstructing it from available
information (which may or may not produce the exact same result, as
different tools may have differences in their heuristics and assumptions
about topologies), topotools will write out incomplete data. topotools was
deliberately designed to be agnostic to force fields and thus any
information not present cannot be automatically recovered.

axel.

> Thank you.
>
> Miao-Chun
> 

-- 
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.