VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Jun 01 2019 - 18:28:42 CDT

Hi Ligesh, LAMMPS will keep track of how many times atoms cross the unit
cell's boundaries, and VMD will use them to reconstruct unwrapped
coordinates, which are useful if you have molecules.

You can use these packages:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
https://github.com/jhenin/qwrap

On Sat, Jun 1, 2019 at 8:03 AM LIGESH B <ligeshkannur178_at_gmail.com> wrote:

> Dear VMD Users,
> I have simulated a polymer network system in LAMMPS. I have used the
> 'bond' atom_style available in LAMMPS for the polymer network. I used the
> Langevin thermostat in the NVE ensemble. I have defined a Periodic boundary
> condition as well. So when I am visualizing the LAMMPS trajectory for the
> system after some time the whole network is moving out of the defined
> periodic boundary box (I have used pbc box in Tk Console to view the
> defined box). I have checked the coordinates of the trajectory which shows
> throughout the simulation the coordinates values are inside the defined box
> range. So why the visualization in VMD shows the system moving out of the
> box?
> All the coordinates in the trajectory file are within the defined PBC box
> range. How one can ensure the system stays inside the box other than
> visualizing it and cross verifying with the trajectory points?
>
> Please help me with this...
>
>
> Thank You.
>
> Regards,
> Ligesh
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin