VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Apr 11 2016 - 13:12:20 CDT

On Mon, Apr 11, 2016 at 1:45 PM, ahmed sengab <sengab_at_aucegypt.edu> wrote:

> Hi,
>
> I am trying to visualize two polymer chains in vmd. My file extension is
> .lammpstrj. VMD add extra bonds that don't exist between the two chains and
> the atoms coordinates are changed, although I checked the .lammprtrj file
> and the coordinates are correct.
>

​as for the bonds, LAMMPS trajectory files do not contain any bond
information, so VMD has to guess, or you have to tell VMD to not guess any
bonds at all when loading the file. VMD bond guessing uses a heuristic
based on atom name conventions for PDB files​, if your file doesn't contain
that information, VMD's guesses can be very bad.

​as for the coordinate change, does your trajectory​ file contain image
flags? then the LAMMPS molfile plugin will reconstruct the corresponding
unwrapped coordinates.
if this is not the case, you have to provide an example file and explain
how you detect that the coordinates are changed.

please also explain, what both of these issues have to do with "atom id
change".

thanks,
     axel.

>
> Regards,
> Ahmed Sengab
> 

-- 
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.