From: Axel Kohlmeyer (
Date: Fri Mar 30 2012 - 12:46:52 CDT

On Fri, Mar 30, 2012 at 12:10 PM, Denis Davydov
<> wrote:
> Dear VMD users,
> I have a question with regards to 'bondsrecalc' command.
> Is there a way to force 'bondsrecalc' to create bonds
> treating periodic boundary conditions ?

no. you'd have to first replicate your coordinates
and then determine which bonds to atoms are bonds
to images and map them back to the original.


> I input data using 'topo readlammpsdata charge' and
> would like to set up bonds, and then - angles using
> 'topo guessangles'
> p/s/ I'm creating an input to LAMMPS for a-quartz with
> defined bonds/angles.
> Thank you in advance,
> Kind regards,
> Denis.

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.