VMD-L Mailing List

From: LIGESH B (ligeshkannur178_at_gmail.com)
Date: Sat Jun 01 2019 - 06:38:18 CDT

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