Problem While Visualising the Trajectory File from Simulation

Dear LAMMPS 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.


This is just a feature of the visualizer and there is absolutely nothing wrong here.


This is just a feature of the visualizer and there is absolutely nothing wrong here.

Hi Ray
It wasn't clear to me if that Ligesh was complaining about the visualizer.
It sounded more like he objected to the fact that the center-of-mass
of his system was moving.
    I was not sure what to say in reply, other than:
Ligesh: Why would you expect the center of mass to remain stationary?

There are fixes which can stop this from happening, such as:
... but I'm not sure this is useful, other than to make it easier to
render movies that don't jump around and look nice.

Regarding the visualization method, ...
I personally prefer using OVITO instead of VMD for visualizing this
kind of system because it will not draw bonds that stretch across the
simulation box. When you have long polymers (longer than the
simulation box size), VMD does a terrible job visualizing these
systems. You're only choice is to show the entire polymer as a single
long molecule.. Ovito allowsyou to cut molecules (or polymers)
wherever they cross the simulation box boundary without drawing ugly
bonds which stretch across the simulation box.

Hope this helps


Andrew, VMD has a dynamic bonds representation, that does not draw bonds across PBC.


Thank You all for your help and comments.
Sir, I got your point. So basically I try to say that if the coordinates in trajectory files are within the PBC limit then also in VMD it shows the system or a portion of the system moving out of the simulation box. Thats, why I asked, is it due to anything wrong in the simulation method or an issue with the VMD representation.

Thank You