VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Aug 14 2008 - 16:24:13 CDT

On Thu, Aug 14, 2008 at 3:25 PM, nicholas lee <nicholjl_at_usc.edu> wrote:
> Hi,
>
> I'm relatively new to VMD. I want to specify bonds between atoms in a LAMMPS trajectory file so they appear in VMD.
> I tried this under "Graphics" -> "Representations" -> "Dynamic Bonds" -> "Distance cut-off" but no matter how large I set the cutoff distance the atoms do not connect. What should I do instead?

have a look at the vmd scripts in the lmp2vmd subdirectory of the
tools directory of the
lammps distribution. standard lammps trajectory files (the ones that
vmd supports) do not
contain any bonding information and atom name info. those scripts
allow you to set/recover
them from the lammps data file and equivalent sources.

cheers,
    axel.

>
> Thanks in advance for your help.
>
> Nicholas J. Lee
>
> 

-- 
=======================================================================
Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
 Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.